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Title: A differential evolution approach to feature selection in genomic prediction
Creator: Whalen, Ian
Date: 2018
Collection: Electronic Theses & Dissertations
Description: The use of genetic markers has become widespread for prediction of genetic merit in agricultural applications and is a beginning to show promise for estimating propensity to disease in human medicine. This process is known as genomic prediction and attempts to model the mapping between an organism's genotype and phenotype. In practice, this process presents a challenging problem. Sequencing and recording phenotypic traits are often expensive and time consuming. This leads to datasets often...
Show moreThe use of genetic markers has become widespread for prediction of genetic merit in agricultural applications and is a beginning to show promise for estimating propensity to disease in human medicine. This process is known as genomic prediction and attempts to model the mapping between an organism's genotype and phenotype. In practice, this process presents a challenging problem. Sequencing and recording phenotypic traits are often expensive and time consuming. This leads to datasets often having many more features than samples. Common models for genomic prediction often fall victim to overfitting due to the curse of dimensionality. In this domain, only a fraction of the markers that are present significantly affect a particular trait. Models that fit to non-informative markers are in effect fitting to statistical noise, leading to a decrease in predictive performance. Therefore, feature selection is desirable to remove markers that do not appear to have a significant effect on the trait being predicted. The method presented here uses differential evolution based search for feature selection. This study will characterize differential evolution's efficacy in feature selection for genomic prediction and present several extensions to the base search algorithm in an attempt to apply domain knowledge to guide the search toward better solutions.
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Title: FITNESS EFFECTS OF KINSHIP DEPEND ON ECOLOGICAL CONTEXT IN THE AMERICAN TOAD (ANAXYRUS AMERICANUS)
Creator: Garnett, Sara Christine
Date: 2018
Collection: Electronic Theses & Dissertations
Description: Studies of cooperation often ask how variation in kinship impacts the inclusive fitness payoffs of altruism. Hamilton’s rule defines this as a function of cooperation's costs and benefits, which in principle can vary widely across ecological contexts. In this dissertation, I address how kinship influences fitness, how selection balances fitness costs and benefits, and how the effects of kinship modulate the effects of other aspects of an organism’s environment using the American toad system....
Show moreStudies of cooperation often ask how variation in kinship impacts the inclusive fitness payoffs of altruism. Hamilton’s rule defines this as a function of cooperation's costs and benefits, which in principle can vary widely across ecological contexts. In this dissertation, I address how kinship influences fitness, how selection balances fitness costs and benefits, and how the effects of kinship modulate the effects of other aspects of an organism’s environment using the American toad system. I first asked whether tadpoles use chemical cues to perceive differences in relatedness and whether this variation affects the response of several fitness proxies to environmental cues. I found that tadpole growth rates differed in response to cues of resource and kinship environment. In another experiment, growth rate differed based on cues of relative size, with larger tadpoles outperforming smaller partners. This was affected by kinship, at least for smaller tadpoles, who grew more rapidly with a sibling. This indicates that chemical cues communicate information necessary for tadpoles to perceive aspects of their environment, which interact with relatedness to affect fitness.I then investigated whether relatedness influences growth and development in experimental groups of tadpoles, and whether other factors – such as density and nutrient availability – impact the fitness benefits of grouping with kin. In our experiments, groups composed of full-sib kin reached metamorphosis faster and at a larger size than mixtures of different sib groups. The benefits of these fitness components were significant in more competitive, resource-scarce environments, but negligible in less-competitive, resource-abundant environments. Kinship and resource abundance have an interactive effect on the fitness components we measured. Finally, I assessed tadpole aggregation preferences for kin compared to non-kin in the presence and absence of predator cues. In the presence of predator cues, tadpoles may be more likely to choose kin over non-kin. While increased body mass might result in a tadpole being more likely to avoid conspecifics in the presence of predator cues, we saw that larger tadpoles potentially increased the probability of choosing kin over non-kin. While these results were not significant, indicating that predator avoidance is likely not the primary driver of kin aggregation behavior in this species, they are suggestive of a kin-selected benefit to grouping.Taken together, these results help us understand the contexts in which we might expect relatedness to affect fitness, which could further contribute to our understanding of the evolution of social behavior. This emphasizes that the fitness benefits of kin-directed behavior are not identical in all circumstances, and that the ratio of costs to benefits may drive the evolution of different strategies depending on the environment.
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Title: Genome-wide association study reveals genes associated with mite recruitment phenotypes in the domesticated grapevine (vitis vinifera
Creator: LaPlante, Erika R.
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Plants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and...
Show morePlants in the grape genus Vitis have varying densities of trichomes and mite-domatia on their leaves, which facilitate the recruitment, retention, and reproduction of beneficial mites. By increasing the abundance of mites on grape leaves, these phenotypes promote a defense mutualism contributing to the control of grape pests and pathogens. Identification of the genes controlling these phenotypes would inform our understanding of the genetics underlying mite-plant mutualistic interactions and could lead to breeding domesticated Vitis vinifera L. varieties that are naturally defended against pathogens. Little is known about the genetics underlying mite recruitment phenotypes in Vitis. We conducted a GWAS to determine the genetic architecture of mite recruitment traits in V. vinifera using 399 cultivars from a common garden diversity panel. We investigated eight traits previously established in the literature associated with an increase in beneficial mite abundance. We found single nucleotide polymorphisms (SNPs) significantly associated with each mite recruitment trait investigated. Corresponding gene annotations of SNP genetic coordinates revealed notable gene associations, including a trichome development gene, and a physiological defense response gene, suggesting these genetic regions may have a large impact on mediating mite-plant interactions in this species. Our findings are among the first to investigate which genes underly ecologically important mutualisms between plants and beneficial mites and suggest promising candidate genes for breeding and genetic editing to increase naturally occurring predator-based defenses in grapes.
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Title: Do latex and resin canals spur plant diversification? : re-examining a classic example of escape and radiate coevolution
Creator: Foisy, Michael
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven's 'escape-and-radiate' hypothesis of co-evolution. However, it has been nearly three decades since these plant defenses have been examined as key innovations, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. I gathered data on...
Show moreThe association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven's 'escape-and-radiate' hypothesis of co-evolution. However, it has been nearly three decades since these plant defenses have been examined as key innovations, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding. I gathered data on latex and resin canals across 345 families and 986 genera of vascular plants and conducted a multi-scale test of the association between these traits and lineage diversification rates. At a broad scale (across clades), I used sister-clade comparisons to test whether 28 canal-bearing clades had higher net diversification rates than their canal-lacking sister clades. At a finer scale (within clades), I used ancestral state reconstructions and phylogenetic models of lineage diversification rates to examine the relationship between trait evolution and the timing of diversification rate shifts in two better-characterized clades - Araceae and Papaveraceae. At both scales of analyses, I found poor support for the predicted relationship between diversification and the evolution of latex and resin canals. This re-examination reveals that there is no longer strong evidence for latex or resin canals as general, consistently replicable drivers of species diversity across plants. However, I could not rule out a relationship in all groups, and therefore argue that theoretical and empirical work aimed at understanding ecological factors that condition 'escape-and-radiate' dynamics will allow for more nuanced tests of the hypothesis in the future.
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Title: The Evolutionary Origins of Cognition : Understanding the early evolution of biological control systems and general intelligence
Creator: Carvalho Pontes, Anselmo
Date: 2021
Collection: Electronic Theses & Dissertations
Description: In the last century, we have made great strides towards understanding natural cognition and recreating it artificially. However, most cognitive research is still guided by an inadequate theoretical framework that equates cognition to a computer system executing a data processing task. Cognition, whether natural or artificial, is not a data processing system; it is a control system.At cognition's core is a value system that allows it to evaluate current conditions and decide among two or more...
Show moreIn the last century, we have made great strides towards understanding natural cognition and recreating it artificially. However, most cognitive research is still guided by an inadequate theoretical framework that equates cognition to a computer system executing a data processing task. Cognition, whether natural or artificial, is not a data processing system; it is a control system.At cognition's core is a value system that allows it to evaluate current conditions and decide among two or more courses of action. Memory, learning, planning, and deliberation, rather than being essential cognitive abilities, are features that evolved over time to support the primary task of deciding “what to do next”. I used digital evolution to recreate the early stages in the evolution of natural cognition, including the ability to learn. Interestingly, I found cognition evolves in a predictable manner, with more complex abilities evolving in stages, by building upon previous simpler ones. I initially investigated the evolution of dynamic foraging behaviors among the first animals known to have a central nervous system, Ediacaran microbial mat miners. I then followed this up by evolving more complex forms of learning. I soon encountered practical limitations of the current methods, including exponential demand of computational resources and genetic representations that were not conducive to further scaling. This type of complexity barrier has been a recurrent issue in digital evolution. Nature, however, is not limited in the same ways; through evolution, it has created a language to express robust, modular, and flexible control systems of arbitrary complexity and apparently open-ended evolvability. The essential features of this language can be captured in a digital evolution platform. As an early demonstration of this, I evolved biologically plausible regulatory systems for virtual cyanobacteria. These systems regulate the cells' growth, photosynthesis and replication given the daily light cycle, the cell's energy reserves, and levels of stress. Although simple, this experimental system displays dynamics and decision-making mechanisms akin to biology, with promising potential for open-ended evolution of cognition towards general intelligence.
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Title: Developing Reverse Genetic Tools in Weakly Electric Fish : Investigating Electric Organ in vivo scn4aa Function Through CRISPR Knockouts and Morpholino Knockdowns
Creator: Constantinou, Savvas James
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The ability to determine gene function allows research to progress at one of the finest scales in biology and is a goal in electric fish research. Reverse genetics allows researchers to determine gene function and would aid the electric fish community in beginning to answer some of the broadest and most complicated questions in biology such as linking genotype to phenotype and understanding the processes that lead to biological diversity. In this dissertation, I describe the development of...
Show moreThe ability to determine gene function allows research to progress at one of the finest scales in biology and is a goal in electric fish research. Reverse genetics allows researchers to determine gene function and would aid the electric fish community in beginning to answer some of the broadest and most complicated questions in biology such as linking genotype to phenotype and understanding the processes that lead to biological diversity. In this dissertation, I describe the development of two major reverse genetic tools for use in the electric fish system: CRISPR/Cas9 genome editing and morpholinos. To develop these tools, I also produced protocols for in-vitro breeding, husbandry, and single-cell embryo microinjections. In the first chapter, I describe in-vitro breeding, husbandry, and single-cell embryo microinjections and demonstrate that CRISPR/Cas9 is a promising tool for future electric fish research by targeting nonsense mutations to scn4aa in the mormyrid Brienomyrus brachyistius and gymnotiform Brachyhypopomus gauderio, two independently evolved lineages of weakly electric fish, resulting in a reduction in the electric organ discharge amplitude. In the second chapter, I provide electric fish researchers with a detailed analysis of our many successes and failures applying CRISPR/Cas9 methods to this system and discuss future suggestions on how to best apply them to novel electric fish research. In the third chapter, I describe my efforts to utilize vivo-morpholinos in mormyrid electric fish. While a single early pilot study I performed demonstrated vivo-morpholinos can reduce target gene mRNA levels and cause a phenotypic effect, my efforts to replicate these findings demonstrate inconsistent performance: control vivo-morpholino and scn4aa targeting vivo-morpholino injected fish had indistinguishable effects on electric organ discharge amplitude. Due to additional concerns of toxicity, I suggest morpholinos are not an ideal reverse genetic tool in Brienomyrus brachyistius and should only be utilized for future research with caution.
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Title: MECHANISMS UNDERLYING DESICCATION RESISTANCE IN DROSOPHILA SPECIES
Creator: Wang, Zinan
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Adaptation to various and extreme environments is key to long-term species persistence. Reducing water loss is important for organisms adapting to different terrestrial environments. In Drosophila fruit flies and other terrestrial insects, their small body size and large surface areas to volume ratios make them vulnerable to desiccation stress. Their ability to prevent water loss is crucial for their survival. Previous studies have suggested that cuticular water loss accounts for the majority...
Show moreAdaptation to various and extreme environments is key to long-term species persistence. Reducing water loss is important for organisms adapting to different terrestrial environments. In Drosophila fruit flies and other terrestrial insects, their small body size and large surface areas to volume ratios make them vulnerable to desiccation stress. Their ability to prevent water loss is crucial for their survival. Previous studies have suggested that cuticular water loss accounts for the majority of water loss in insects and hypothesized that differences in cuticular hydrocarbon (CHC) content accounted for differences in desiccation resistance between mesic and desert species. However, the specific association between different CHC components and desiccation has not been established, and the genetic mechanisms underlying the evolution of these CHC components that confer high desiccation resistance have not been elucidated. This dissertation investigated how the evolution of CHCs in insects affected desiccation resistance and elucidates the genetic mechanisms underlying their evolution. With a comprehensive association study of desiccation resistance and CHCs in 46 Drosophila species and 4 species in closely-related genera, the analyses showed that mbCHC chain lengths were important predictors of desiccation resistance and longer mbCHCs contributed to higher desiccation resistance. This dissertation further investigated the genetic and molecular mechanisms underlying longer chain mbCHCs and higher desiccation resistance in a desert Drosophila species, Drosophila mojavensis. A fatty acyl-CoA elongase gene, mElo (methyl-branched CHC Elongase), was identified in Drosophila species for the elongation of mbCHCs. Overexpression experiments in D. melanogaster demonstrated that coding changes in mElo from D. mojavensis lead to longer mbCHCs and higher desiccation resistance. Further experiments using CRISPR-Cas9 to knock out mElo from D. mojavensis showed that knockout of this gene decreased the production of the longest mbCHCs and significantly reduced desiccation resistance at their ecological-relevant temperature. Results from this dissertation elucidate the molecular and evolutionary mechanisms that enable species to reduce water loss and maintain water balance as our planet gets warmer and more arid in the next few decades.
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Title: Evolving Phenotypically Plastic Digital Organisms
Creator: Lalejini, Alexander
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The ability to dynamically respond to cues from the environment is a fundamental feature of most adaptive systems. In biological systems, changes to an organism based on environmental cues is called phenotypic plasticity. Indeed, phenotypic plasticity underlies many of the adaptive traits and developmental patterns found in nature and serves as a key mechanism for responding to spatially or temporally variable environments. Most computer programs require phenotypic plasticity, as they must...
Show moreThe ability to dynamically respond to cues from the environment is a fundamental feature of most adaptive systems. In biological systems, changes to an organism based on environmental cues is called phenotypic plasticity. Indeed, phenotypic plasticity underlies many of the adaptive traits and developmental patterns found in nature and serves as a key mechanism for responding to spatially or temporally variable environments. Most computer programs require phenotypic plasticity, as they must respond dynamically to stimuli such as user input, sensor data, et cetera. As such, phenotypic plasticity also has practical applications in genetic programming, wherein we apply the natural principles of evolution to automatically synthesize computer programs rather than writing them by hand. In this dissertation, I achieve two synergistic aims: (1) I use populations of self-replicating computer programs (digital organisms) to empirically study the conditions under which adaptive phenotypic plasticity evolves and how its evolution shapes subsequent evolutionary outcomes; and (2) I transfer insights from biology to develop novel genetic programming techniques in order to evolve more responsive (i.e., phenotypically plastic) computer programs. First, I illustrate the importance of mutation rate, environmental change, and partially-plastic building blocks for the evolution of adaptive plasticity. Next, I show that adaptive phenotypic plasticity stabilizes populations against environmental change, allowing them to more easily retain novel adaptive traits. Finally, I improve our ability to evolve phenotypically plastic computer programs with three novel genetic programming techniques: (1) SignalGP, which provides mechanisms to control code expression based on environmental cues, (2) tag-based genetic regulation to adjust code expression based on current context, and (3) tag-accessed memory to provide more dynamic mechanisms for storing data.
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Title: Replaying Life's Virtual Tape : Examining the Role of History in Experiments with Digital Organisms
Creator: Bundy, Jason Nyerere
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Evolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not...
Show moreEvolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not everyone was convinced. Some believed that chance was the primary driver of evolutionary change, while others insisted that natural selection was the most powerful influence. Since then, “replaying life’s tape” has become a core method in experimental evolution for measuring the relative contributions of adaptation, chance, and history. In this dissertation, I focus on the effects associated with history in evolving populations of digital organisms—computer programs that self-replicate, mutate, compete, and evolve in virtual environments. In Chapter 1, I discuss the philosophical significance of Gould’s thought experiment and its influence on experimental methods. I argue that his thought experiment was a challenge to anthropocentric reasoning about natural history that is still popular, particularly outside of the scientific community. In this regard, it was his way of advocating for a “radical” view of evolution. In Chapter 2—Richard Lenski, Charles Ofria, and I describe a two-phase, virtual, “long-term” evolution experiment with digital organisms using the Avida software. In Phase I, we evolved 10 replicate populations, in parallel, from a single genotype for around 65,000 generations. This part of the experiment is similar to the design of Lenski’s E. coli Long-term Evolution Experiment (LTEE). We isolated the dominant genotype from each population around 3,000 generations (shallow history) into Phase I and then again at the end of Phase I (deep history). In Phase II, we evolved 10 populations from each of the genotypes we isolated from Phase I in two new environments, one similar and one dissimilar to the old environment used for Phase I. Following Phase II, we estimated the contributions of adaptation, chance, and history to the evolution of fitness and genome length in each new environment. This unique experimental design allowed us to see how the contributions of adaptation, chance, and history changed as we extended the depth of history from Phase I. We were also able to determine whether the results depended on the extent of environmental change (similar or dissimilar new environment). In Chapter 3, we report an extended analysis of the experiment from the previous chapter to further examine how extensive adaptation to the Phase I environment shaped the evolution of replicates during Phase II. We show how the form of pleiotropy (antagonistic or synergistic) between the old (Phase I) and new (Phase II) habitats was influenced by the depth of history from Phase I (shallow or deep) and the extent of environmental change (similar or dissimilar new environment). In the final chapter Zachary Blount, Richard Lenski, and I describe an exercise we developed using the educational version of Avida (Avida-ED). The exercise features a two-phase, “replaying life’s tape” activity. Students are able to explore how the unique history of founders that we pre-evolved during Phase I influences the acquisition of new functions by descendent populations during Phase II, which the students perform during the activity.
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Title: THE TRANSCRIPTOMIC AND EPIGENOMIC RESPONSE OF KOCHIA SCOPARIA TO SUBLETHAL GLYPHOSATE
Creator: Claucherty, Carly Abbegail
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Weed populations respond and adapt to herbicide stress by evolving resistance. Glyphosate resistance is primarily caused by the amplification of the target site gene, EPSPS, where multiple copies produce a large enough protein pool so that field rates do not kill the plant. This mechanism has evolved independently in at least nine divergent weed species. It has been demonstrated that EPSPS gene duplication may be transposon mediated in Kochia scoparia. A key regulator of transposable element ...
Show moreWeed populations respond and adapt to herbicide stress by evolving resistance. Glyphosate resistance is primarily caused by the amplification of the target site gene, EPSPS, where multiple copies produce a large enough protein pool so that field rates do not kill the plant. This mechanism has evolved independently in at least nine divergent weed species. It has been demonstrated that EPSPS gene duplication may be transposon mediated in Kochia scoparia. A key regulator of transposable element (TE) activity is DNA methylation. The role of the epigenome and subsequent transcriptome in transient responses to herbicides of their primary target, weeds, is not well understood In this study, we performed RNA-Seq and bisulfite sequencing on leaf tissue from glyphosate-sensitive kochia before and three weeks after treatment with two sublethal doses to determine if glyphosate causes hypomethylation of the genome, allowing for the activation of transposons and upregulation of stress-related genes. Our results shows that overall gene expression was suppressed by glyphosate and increases in CHH methylation through development were also ceased. We did not observe significant global changes in cytosine methylation, and overall responses were stochastic. When combining the two datasets together, there was no direct correlation between changes in methylation and changes in gene expression suggesting that DNA methylation is not the primary cause of differential expression in our study. Our results broaden the knowledge pool of weedy species epigenomics and aid in understanding the contribution of DNA methylation to plant resilience in response to herbicide stress.
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Title: Diversity of South American ambrosia beetles (Curculionidae : Scolytinae: Xyleborini) and their fungal partners
Creator: Osborn, Rachel Kathryn
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Ambrosia beetles from the tribe Xyleborini (Coleoptera: Curculionidae: Scolytinae) small, haplodiploid beetles that farm nutritional fungi on the walls of tunnels they excavate in the xylem of dead or nearly dead trees. These biological traits make them successful participants in worldwide wooded ecosystems and facilitate their human-mediated invasion beyond their native ranges. A minority of these introduced species are classified as pests because of the physical damage they cause to their...
Show moreAmbrosia beetles from the tribe Xyleborini (Coleoptera: Curculionidae: Scolytinae) small, haplodiploid beetles that farm nutritional fungi on the walls of tunnels they excavate in the xylem of dead or nearly dead trees. These biological traits make them successful participants in worldwide wooded ecosystems and facilitate their human-mediated invasion beyond their native ranges. A minority of these introduced species are classified as pests because of the physical damage they cause to their plant hosts, or because they vector pathogenic fungi that infect ornamental, lumber, and forest trees. Most of the current knowledge on the diversity of xyleborine beetles and their fungi centers around species found in North America, Asia, and Europe. Little is known about the ambrosia partnerships in the Neotropics, which is concerning because South America is a strong trading partner with the US and the potential for new invasive Xyleborini to be imported from this area is significant. Continuing forest damage caused by invasive Xyleborini/fungi inspires robust research efforts to describe these symbionts and document their biological traits. Considerable efforts are required to enhance such endeavors in underrepresented regions such as South America and Africa. To increase understanding of the South American Xyleborini and their associated fungi, I compiled current knowledge of their historical and contemporary taxonomic records, biological records, and ecological studies. I also completed surveys throughout Ecuador to collect beetles and fungi. Molecular analysis of fungi isolated from Ecuadorian beetles reveals that several Coptoborus species associate with Fusarium fungi, including the ambrosia Fusarium Clade (AFC) that has previously been recovered from Euwallacea spp. and Xyleborus ferrugineus in Central America, Florida, California, Israel, and Asia. Examination of the morphology of some South American xyleborine specimens previously classified as Coptoborus spp. suggests a high similarity to Xyleborus spp. from Africa. Phylogenetic analysis of these South American and African beetles as well as morphological assessment of additional specimens necessitates the designation of a new genus Xenoxylebora gen. nov. containing species endemic to both continents. This unusual distribution demonstrates the ability of these ambrosia beetles to survive long-distance trans-oceanic dispersal.
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