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Title: Analytical paleontology : patterns of taxonomic extinction
Creator: Younker, Jean Lower, 1946-
Date: 1976
Collection: Electronic Theses & Dissertations

Title: Developmental and functional constraints on phenotypic covariation during growth and evolution
Creator: Zelditch, Miriam Leah
Date: 1987
Collection: Electronic Theses & Dissertations

Title: Origin and geochemical evolution of the Michigan basin brine
Creator: Wilson, Timothy Peter
Date: 1989
Collection: Electronic Theses & Dissertations

Title: The application of a co-evolutionary perspective to the case of deer hunting ethoses within a human ecosystem
Creator: Andersen, Thomas A. (Thomas Andrew)
Date: 2001
Collection: Electronic Theses & Dissertations

Title: The ecology and evolution of elevation range limits in monkeyflowers (mimulus cardinalis and M. Lewisii)
Creator: Angert, Amy Lauren
Date: 2005
Collection: Electronic Theses & Dissertations

Title: Analyzing biological complexity with digital organisms
Creator: Huang, Wei
Date: 2005
Collection: Electronic Theses & Dissertations

Title: Evolution and ecological specialization of a Shewanella baltica population
Creator: Deng, Jie
Date: 2011
Collection: Electronic Theses & Dissertations
Description: Studying how bacterial strains diverge over time and how divergence leads to specialization to new environmental niches is important for understanding the dynamics of environmental communities. I studied these questions using a collection of 46 Shewanella baltica strains isolated over a period of 12 years from the Gotland Deep in the central Baltic Sea, which is characterized by the presence of a stable redox gradient over 140 m in depth. I used several experimental and computational methods...
Show moreStudying how bacterial strains diverge over time and how divergence leads to specialization to new environmental niches is important for understanding the dynamics of environmental communities. I studied these questions using a collection of 46 Shewanella baltica strains isolated over a period of 12 years from the Gotland Deep in the central Baltic Sea, which is characterized by the presence of a stable redox gradient over 140 m in depth. I used several experimental and computational methods to explore the genetic and phenotypic profiles of these strains and determined whether these profiles could be explained by the conditions at their sites of isolation. Specifically, genotyping by both single gene-based and multi-locus sequence typing (MLST) indicated specialization across the redox gradient and over time. Versatility in anaerobic respiration, for example, the ability to respire thiosulfate, was correlated with the redox gradient, while versatility in carbon source utilization was correlated with specialization over time. Comparative Genomic Hybridization (CGH) revealed a heterogeneous distribution of genes across S. baltica genomes, where genes potentially important for specialization both over the redox gradient and over time were identified. Further mechanistic investigation of their evolution provided evidence of horizontal gene transfer in the S. baltica genomes, whereas predicted recent recombination among strains from two lineages was also supported by this larger dataset. The differential fitness of S. baltica strains under particular redox conditions was determined from competition assays, where competed strains were labeled with gfp and cfp and the population dynamics during competition was measured by flow cytometry. The two competed genotypes were separated by flow cytometry and their transcriptomes analyzed by RNA-Seq which showed differential expression in response to the nitrate condition as well as to the competitor strain. By integrating these different types of information, I determined that specialization has occurred in this S. baltica population both over the redox gradient and over time, and that the genomic plasticity as well as the extensive gene exchange has facilitated the specialization process. Overall, I used S. baltica as a model to provide insights into fundamental questions about the interactions among bacterial genomics, physiology, and habitat (ecology).
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Title: The effect of temperature on the ecology, evolution, and biogeography of phytoplankton
Creator: Thomas, Mridul Kanianthara
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Temperature is a fundamental driver of biological dynamics, but we do not know how it shapes the physiology and ecology of any community across global temperature gradients. Here I examine the influence of temperature on phytoplankton, which are extremely sensitive to changes in environmental conditions and play a critical role in global food webs and biogeochemical cycles. I address how global variation in temperature regimes has shaped distributions of phytoplankton temperature traits,...
Show moreTemperature is a fundamental driver of biological dynamics, but we do not know how it shapes the physiology and ecology of any community across global temperature gradients. Here I examine the influence of temperature on phytoplankton, which are extremely sensitive to changes in environmental conditions and play a critical role in global food webs and biogeochemical cycles. I address how global variation in temperature regimes has shaped distributions of phytoplankton temperature traits, identifying patterns of adaptation as well as differences in how major functional groups respond to environmental temperature gradients. I also show that due to the asymmetric cost of exceeding the optimal temperature and the traits of tropical species, ocean warming this century may drive a reduction in the diversity of tropical phytoplankton communities in the absence of evolutionary adaptation. Tropical phytoplankton species may persist, however, by poleward migration, bringing them into competition with temperate species. Our study of the temperature traits of an invasive cyanobacterium supports the idea that rising temperatures will increase the probability of invasion by tropical and subtropical species into temperate environments. Predicting these invasions, however, is a challenge that requires us to model the phytoplankton community dynamics in complex natural environments. This will require a mechanistic understanding of how temperature interacts with important resources such as nutrients and light to influence growth. To address this, I have developed and tested a model describing how temperature and nutrients interact to affect growth rates. Our experimental tests confirm a novel prediction: that optimum temperature for growth is a saturating function of nutrient concentration. Together, this work forms a foundation from which we can build predictive models of how environmental warming will affect population and community dynamics across broad spatial scales.
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Title: Fitness tradeoffs can contribute to the maintenance of variation in personality traits in largemouth bass (Micropterus salmoides)
Creator: Ballew, Nicholas G.
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Studies examining selection and fitness differences between phenotypes are essential for our understanding of evolutionary processes. Although many studies have examined fitness effects of morphological and life-history traits, studies of selection on personality traits are much less common. This has been due, in part, to the fact that personality is not easily characterized into phenotypes. In addition, personality has historically been viewed as highly plastic and therefore less likely to...
Show moreStudies examining selection and fitness differences between phenotypes are essential for our understanding of evolutionary processes. Although many studies have examined fitness effects of morphological and life-history traits, studies of selection on personality traits are much less common. This has been due, in part, to the fact that personality is not easily characterized into phenotypes. In addition, personality has historically been viewed as highly plastic and therefore less likely to be under the direct influence of selection. However, recent studies suggest that personality is often consistent over biologically meaningful time periods. If personality traits are consistent across development, they have the potential to affect fitness through impacts on survival at the juvenile stage and reproductive success at the adult stage. Thus, personality traits may have a range of effects on fitness, some of which could result in tradeoffs. Further, personality likely determines an individual's vulnerability to human capture and harvest in a variety of contexts, which means human actions could alter the effects of personality on fitness. For example, a fish's personality may affect its vulnerability to capture by recreational angling, which could alter the relationships between personality and survival and reproductive success. Moreover, if personality traits are heritable, angling could result in the evolution of personality traits in angled populations, which could have ecological consequences. Consequently, studies to explain how personality is generated and maintained by evolution are greatly needed. Here, I address the fitness consequences of multiple personality traits across life stages and their heritability in largemouth bass (Micropterus salmoides). Further, I address how angling could alter these fitness effects. To quantify personality and investigate its consistency, bass were observed in the laboratory under experimental behavioral contexts at age-1, age-3, age-4, and age-5. Bass behavior was observed in four contexts: 1) a novel environment, 2) a familiar and safe environment, 3) a social environment (mirror-test), and 4) an environment in which both food and a predator were present. To quantify the fitness effects across life stages of the personality traits uncovered in the experimental behavioral assays, experiments were conducted in outdoor ponds on juvenile survivorship and on adult reproductive success. Further, bass were subjected to one of three angling contexts: 1) a mesocosm context, 2) an outdoor pond context, and 3) an outdoor pond context with casts made directly onto bass nests. Lastly, personality was quantified in two generations of bass to assess personality heritability. The results showed that bass have context-specific personality traits that underlie the expression of behavior in each of the four contexts investigated and that the context-specific traits are sub-modules of a context-general trait, which was identified as boldness. The boldness trait, as well as some of the context-specific traits, were consistent across multiple years and developmental stages. Bolder juvenile bass had significantly lower survivorship than their conspecifics while adult bass that were larger and bolder had significantly higher reproductive success. Additionally, relationships were found between some of the context-specific traits and juvenile survival and reproductive success. Bolder bass were more vulnerable to angling in the mesocosm context and bolder nesting males were more vulnerable to nest angling. Additional relationships were found between some of the context-specific traits and angling vulnerability. Boldness was the only personality trait that was significantly heritable. The results of this dissertation demonstrate for the first time that personality traits that are consistent across development can affect fitness in multiple ways over the course of an individual's lifetime. In some environments, these fitness effects can result in tradeoffs that could maintain within population variation in personality traits. Further, the results indicate that the selective capture of fish by angling can alter the selective landscape acting on personality traits, which could have significant evolutionary and ecological consequences and could affect the quality of fisheries.
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Title: Using experimental evolution in Drosophila melanogaster to test predictions about the adaptation of prey to a novel predator
Creator: DeNieu, Michael
Date: 2014
Collection: Electronic Theses & Dissertations
Description: One of the primary questions in organismal biology is how evolution has acted to shape the species that we see in nature. Beginning to address this incredibly complex question requires a diverse set of approaches that can be difficult to accomplish in the wild, in part because it requires a relatively robust knowledge of the evolutionary history of given populations. Though it cannot tell us how existing species have evolved, experimental evolution is a powerful tool because it allows one to...
Show moreOne of the primary questions in organismal biology is how evolution has acted to shape the species that we see in nature. Beginning to address this incredibly complex question requires a diverse set of approaches that can be difficult to accomplish in the wild, in part because it requires a relatively robust knowledge of the evolutionary history of given populations. Though it cannot tell us how existing species have evolved, experimental evolution is a powerful tool because it allows one to track phenotypic and genotypic changes in populations over time in response to a controlled selection pressure. By imposing a particular selection pressure on populations with a known origin, I can test hypotheses about organismal evolution generated by studying patterns in nature. Here I will discuss a series of experiments conducted on populations of Drosophila melanogaster that have been evolved under predatory selection by nymphs of the Chinese mantis (Tenodera aridifolia sinensis). I first investigated the ability to use phenotypic selection analysis to determine long term evolutionary outcomes. To do this, I measured selection acting on wing size and shape in the base population and then again in the evolved populations after 30 generations of selection, and used this to determine other important morphological and behavioral traits that have likely been targets of selection. I show that evolutionary trajectories are largely predictable, but that unmeasured traits can have profound effects on evolutionary outcomes. I also test the predictions of the risk allocation hypothesis as it pertains to courtship, aggression, and anti-predator behavior. Unlike many previous studies that have focused on learned responses to predation risk, I tested whether populations evolved under differences in variation in predation risk would evolve behavioral patterns consistent with the risk allocation hypothesis. I found that while the hypothesis captured several important aspects of the evolutionary response, the specific predictions failed to accurately describe the actual outcome. my results suggested that the riskiness of different behavioral types played a large role in determining whether they conformed to the predictions of risk allocation. In my final chapter, I investigate a unique behavior in which flies evolved in the presence of predators reduce their propensity to initiate flight. Though my results cannot conclusively determine the cause of the evolution of this new escape strategy, they do suggest that associations with allometric scaling relationships are important in determining the fitness of the divergent strategies observed in the predator-evolved populations.
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Title: Host-symbiont coevolution in digital and microbial systems
Creator: Zaman, Luis
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Darwin's image of the entangled bank captures foremost the pervasiveness of life as it clothes the earth, but it also captures how intimately species interact and often depend on one another. This interaction is particularly pronounced for obligate parasites, who's livelihoods depend on interactions with their hosts and who's hosts often pay severely. In my thesis, I first demonstrate how antagonistic coevolution in Avida leads to a diverse set of interacting host and parasite phenotypes: a...
Show moreDarwin's image of the entangled bank captures foremost the pervasiveness of life as it clothes the earth, but it also captures how intimately species interact and often depend on one another. This interaction is particularly pronounced for obligate parasites, who's livelihoods depend on interactions with their hosts and who's hosts often pay severely. In my thesis, I first demonstrate how antagonistic coevolution in Avida leads to a diverse set of interacting host and parasite phenotypes: a digital entangled bank. Second, I show how further evolution is embedded within this community context by studying the coevolution of complexity driven by parasites'population genetic memory -- where the diversifying community of parasites "remembers" previously evolved hosts. Continuing to study the intersection of coevolution and community ecology, I investigate the structure of communities produced by the coevolutionary process in Avida. I show that a nested structure of interactions is common in our experiments, which is the same structure often found in natural host-parasite and plant-pollinator communities as well as many phage-bacteria interaction networks. In addition, I show that "growing" networks are nested by virtue of the process of incrementally adding nodes and edges. Thus, coevolution is expected to produce significantly nested communities when compared to random networks. However, the coevolved digital host-parasite networks are significantly more nested than expected from this neutral growth process. The interactions between hosts and their intimately interacting partners are not just parasitic, instead they span a broad range and include many mutualistic interactions. In the last section of my thesis, I study evolution and coevolution along the parasitism-mutualism continuum using a temperate λ phage system that provides its host with access to an otherwise unavailable metabolic pathway. Instead of evolving more mutualistic phage as I predicted, both the phage and bacteria evolved cheating strategies.
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Title: Mating system and the evolution of stamen morphology in the mustard family (Brassicaceae
Creator: Royer, Anne Michelle
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Biotic diversity is characterized by patterns of both divergence and similarity. Both natural selection and constraint may operate to conserve a trait across related species, depending on the ecology of the species. My dissertation investigates the roles of these evolutionary forces in maintaining a family-diagnostic stamen morphology. Flowers in the Brassicaceae (mustard plant family) are characterized by four long and two short stamens within a flower (Zomlefer 1994). Although found in >95%...
Show moreBiotic diversity is characterized by patterns of both divergence and similarity. Both natural selection and constraint may operate to conserve a trait across related species, depending on the ecology of the species. My dissertation investigates the roles of these evolutionary forces in maintaining a family-diagnostic stamen morphology. Flowers in the Brassicaceae (mustard plant family) are characterized by four long and two short stamens within a flower (Zomlefer 1994). Although found in >95% of the genera in the family (Endress 1992), the reason(s) for the widespread conservation of this morphology are not known.Existing adaptive hypotheses for the evolution and the maintenance of tetradynamy address how the trait could increase fitness for outcrossing species. While there is some evidence that tetradynamy is adaptive in self-incompatible members of the Brassicaceae (e.g. Kudo 2003; Conner et al. 2009), how it functions is not clear. Additionally, there have been multiple independent losses of self-incompatibility in the family (Lloyd 1965; Mable et al. 2005), followed in some cases by the evolution of high self-pollination rates (Preston 1986). In these highly selfing species, the maintenance of short stamens, which general appear too short to pollinate the stigma within a flower (Müller 1961), is particularly mysterious. My dissertation unites approaches from evolution, ecology, and genetics to understand the maintenance of short stamens in the Brassicaceae across the full range of mating systems. I investigate the function and morphology of short stamens in three species: the obligately outcrossing wild radish (Raphanus raphanistrum), the highly selfing model plant Arabidopsis thaliana, and A. thaliana's sister species, A. lyrata, which includes both outcrossing and selfing populations.In the outcrossing species Raphanus raphanistrum, I used experimental manipulations in arrays exposed to pollination in the field to show that having more stamens increases male fitness, and female fitness is also affected by stamen treatment. There were some indications that short stamens were more attractive to pollinators at high overall pollinator visitation rates. In the highly selfing model plant Arabidopsis thaliana, I showed that short stamens do not significantly increase fitness. I found many populations, particularly near the southern end of the geographic range, have partially lost the short stamens. Genetic mapping revealed three QTL controlling the number of short stamens, with strong epistasis greatly reducing their individual effects. Ongoing evolutionary loss of non-adaptive short stamens in Arabidopsis thaliana may be slowed by gene interactions, low genetic variance in the north, and an inbreeding mating system. Finally, I investigated the evolution of floral morphology in selfing and outcrossing populations of the mixed-mating Arabidopsis lyrata. I found that while relative investment in female fitness has increased as predicted in selfing populations, predicted changes in size and evolution of short stamens have not yet occurred. This may be consistent with recent evolution of selfing, continued facilitation of pollination by insects, and/or constraint on the evolution of short stamens.
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Title: Floral evolution in milkweeds : evidence for selection past and present
Creator: La Rosa, Raffica Jeanne
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Adaptation is an important process that allows species to utilize new habitats and to avoid extinction, contributing to the biodiversity we find on the planet. Many flowering plants rely on animals for pollination; the floral traits that are adaptive for pollination are those that influence attraction, rewards, or efficiency. Milkweeds (Asclepias) have unusual floral structures that consist of a gynostegium surrounded by five nectar-filled hoods. In many species, a horn develops from the...
Show moreAdaptation is an important process that allows species to utilize new habitats and to avoid extinction, contributing to the biodiversity we find on the planet. Many flowering plants rely on animals for pollination; the floral traits that are adaptive for pollination are those that influence attraction, rewards, or efficiency. Milkweeds (Asclepias) have unusual floral structures that consist of a gynostegium surrounded by five nectar-filled hoods. In many species, a horn develops from the inside base of each hood. Pollen grains are packaged into waxy packets (pollinia) and are positioned in the wall of the gynostegium. For fertilization, pollinia must be removed by pollinators and inserted into stigmatic openings in the wall of the gynostegium between adjacent hoods; pollination is carried out passively by a wide variety of pollinators that are almost entirely all insects. Milkweeds are hermaphroditic, so it is possible for the floral traits to be adaptive for male fitness, female fitness, or both. The floral diversity across Asclepias is astounding. My dissertation investigates if and how the floral structures are adaptive, and if the variation among species is the result of natural selection. I used two complementary approaches. For the first approach, I used contemporary measures of selection and functional studies to focus on the process of adaptation in five species of North American Asclepias. Selection works on intraspecific variation within traits and the effect of that variation on fitness. I also utilized paternity analyses in two species to measure selection through male fitness. For the second approach, I used phylogenetic methods to find signatures of past selection on traits across more than one hundred North American Asclepias species. Phylogenetic comparative methods focus on patterns of interspecific variation. I used tests of correlated evolution between pairs of traits, or traits and pollinators, to investigate functional relationships and possible selective agents. I also tested for convergent evolution, which can demonstrate adaptive evolution in response to a similar selective regime. The six floral traits I studied had an effect on fitness, suggesting they are adaptive. I found that many of the floral traits were under significant selection through only one gender, but that the direction of selection was similar across genders, showing little conflict between male and female function or between male and female fitness. I predicted that the size of the hood and gynostegium would influence pollinator attraction, but they were instead more likely to influence the efficiency of pollination. I also found no significant link between female pollination success and female reproductive success in four of the five species, so traits that increased pollen receipt did not in turn affect female fitness, which is consistent with fruit production not being limited by pollen receipt. Using measures of viable seeds produced (annual female fitness) and viable seeds sired (annual male fitness), I determined that selection estimated using total fruit number is a good estimate of selection through viable seeds produced; however, total pollinia removed per plant, a common estimate of male function and fitness in milkweeds is not a good predictor of viable seeds sired. My studies of the gynostegia, hoods, and horns across the phylogeny showed that horn loss likely followed the closure of hoods, suggesting a possible loss of horn function. There were also three convergent floral phenotypes; each may have evolved in response to similar selective regimes. The convergent species provide an excellent starting point for future investigations of possible selective agents.
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Title: An analysis of fitness in long-term asexual evolution experiments
Creator: Wiser, Michael J.
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Evolution is the central unifying concept of modern biology. Yet it can be hard to study in natural system, as it unfolds across generations. Experimental evolution allows us to ask questions about the process of evolution itself: How repeatable is the evolutionary process? How predictable is it? How general are the results? To address these questions, my collaborators and I carried out experiments both within the Long-Term Evolution Experiment (LTEE) in the bacteria Escherichia coli, and the...
Show moreEvolution is the central unifying concept of modern biology. Yet it can be hard to study in natural system, as it unfolds across generations. Experimental evolution allows us to ask questions about the process of evolution itself: How repeatable is the evolutionary process? How predictable is it? How general are the results? To address these questions, my collaborators and I carried out experiments both within the Long-Term Evolution Experiment (LTEE) in the bacteria Escherichia coli, and the digital evolution software platform Avida. In Chapter 1, I focused on methods. Previous research in the LTEE has relied on one particular way of measuring fitness, which we know becomes less precise as fitness differentials increase. I therefore decided to test whether two alternate ways of measuring fitness would improve precision, using one focal population. I found that all three methods yielded similar results in both fitness and coefficient of variation, and thus we should retain the traditional method.In Chapter 2, I turned to measuring fitness in each of the populations. Previous work had considered fitness to change as a hyperbola. A hyperbolic function is bounded, and predicts that fitness will asymptotically approach a defined upper bound; however, we knew that fitness in these populations routinely exceeded the asymptotic limit calculated from a hyperbola fit to the earlier data. I instead used to a power law, a mathematical function that does not have an upper bound. I found that this function substantially better describes fitness in this system, both among the whole set of populations, and in most of the individual populations. I also found that the power law models fit on just early subsets of the data accurately predict fitness far into the future. This implies that populations, even after 50,000 generations of evolution in consistent environment, are so far from the tops of fitness peaks that we cannot detect evidence of those peaks.In Chapter 3, I examined to how variance in fitness changes over long time scales. The among-population variance over time provides us information about the adaptive landscape on which the populations have been evolving. I found that among-population variance remains significant. Further, competitions between evolved pairs of populations reveal additional details about fitness trajectories than can be seen from competitions against the ancestor. These results demonstrate that our populations have been evolving on a complex adaptive landscape.In Chapter 4, I examined whether the patterns found in Chapter 2 apply to a very different evolutionary system, Avida. This system incorporates many similar evolutionary pressures as the LTEE, but without the details of cellular biology that underlie nearly all organic life. I find that in both the most complex and simplest environments in Avida, fitness also follows the same power law dynamics as seen in the LTEE. This implies that power law dynamics may be a general feature of evolving systems, and not dependent on the specific details of the system being studied.
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Title: Sea change. phytoplankton change too? : thermal adaptation of the marine diatom Thalassiosira pseudonana in response to temperature : an evolutionary scenario
Creator: O'Donnell, Daniel Roy
Date: 2018
Collection: Electronic Theses & Dissertations
Description: "Rapid evolution in response to environmental change will likely be a driving force determining the distribution of species across the biosphere in coming decades. This is especially true of microorganisms, many of which may evolve in step with warming, including phytoplankton, the diverse photosynthetic microbes forming the foundation of most aquatic food webs. I tested the capacity of a globally important, model marine diatom Thalassiosira pseudonana , for rapid evolution in response to...
Show more"Rapid evolution in response to environmental change will likely be a driving force determining the distribution of species across the biosphere in coming decades. This is especially true of microorganisms, many of which may evolve in step with warming, including phytoplankton, the diverse photosynthetic microbes forming the foundation of most aquatic food webs. I tested the capacity of a globally important, model marine diatom Thalassiosira pseudonana , for rapid evolution in response to temperature. Selection at 16 and 31°C for 350 generations led to significant divergence in several temperature response traits, demonstrating local adaptation and the existence of tradeoffs associated with adaptation to different temperatures. In contrast, competitive ability for nitrogen (commonly limiting in marine systems), measured after 450 generations of temperature selection, did not diverge in a systematic way between temperatures. After 500 generations of temperature selection, T. pseudonana populations had diverged in their thermal reaction norms for fatty acid composition and in their carbon, nitrogen, phosphorus and chlorophyll a contents. Divergence in C:N:P stoichiometry was not apparent. 31°C-selected populations showed morphological evidence of selection for more efficient nutrient uptake at high temperatures. This study shows how rapid thermal adaptation affects important growth, nutrient uptake and utilization, and cellular physiology and morphology traits in a key marine phytoplankton species, and may thus play a role in long-term physiological, ecological and biogeographic responses to climate change."--Abstract.
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