A5070912354- Evolutionary Game Theory and Cooperation
- Evolution and Genetic Dynamics
- Insect and Arachnid Ecology and Behavior
- Cellular Mechanics and Interactions
- Micro and Nano Robotics
- Vibrio bacteria research studies
- Ecosystem dynamics and resilience
- Plant and animal studies
- Bacterial biofilms and quorum sensing
- Genetics, Aging, and Longevity in Model Organisms
- Genetic diversity and population structure
- Protist diversity and phylogeny
- Genomics and Phylogenetic Studies
- Legionella and Acanthamoeba research
- Machine Learning in Bioinformatics
- Gene Regulatory Network Analysis
- CRISPR and Genetic Engineering
- Physiological and biochemical adaptations
- Biocrusts and Microbial Ecology
- Fungal and yeast genetics research
- Experimental Behavioral Economics Studies
- Aquatic Ecosystems and Phytoplankton Dynamics
- Slime Mold and Myxomycetes Research
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
Massey University
2018-2023
University of Houston
2015-2023
Rice University
2007-2010
Michigan State University
2005-2007
Accurate identification of genetic variants from next-generation sequencing (NGS) data is essential for immediate large-scale genomic endeavors such as the 1000 Genomes Project, and crucial further analysis based on discoveries. The key challenge in single nucleotide polymorphism (SNP) discovery to distinguish true individual (occurring at a low frequency) errors (often occurring frequencies orders magnitude higher). Therefore, knowledge error probabilities base calls essential. We have...
In the social amoeba Dictyostelium discoideum, thousands of cells aggregate upon starvation to form a multicellular fruiting body, and approximately 20% them die stalk that benefits others. The aggregative nature development makes vulnerable exploitation by cheaters, potential for cheating is indeed high. Cells might avoid being victimized if they can discriminate among individuals those are genetically different. We tested how widely amoebae cooperate mixing isolates from different...
Pleiotropy plays a central role in theories of adaptation, but little is known about the distribution pleiotropic effects associated with different adaptive mutations. Previously, we described phenotypic collection independently arising beneficial mutations Escherichia coli. We quantified their fitness glucose environment which they evolved and five novel resource environments. Here use candidate gene approach to associate underlying genetic changes. Among our 27 mutants, identified total 21...
Dictyostelium discoideum is a eukaryotic microbial model system for multicellular development, cell–cell signaling, and social behavior. Key models of evolution require an understanding genetic relationships between individuals across the genome or possibly at specific genes, but nature variation within D. largely unknown. We re-sequenced 137 gene fragments in wild North American strains examined levels patterns nucleotide this species. observe surprisingly low these strains, with mean...
It is generally thought that random mutations will, on average, reduce an organism's fitness because resulting phenotypic changes are likely to be maladaptive. This relationship leads the prediction alter more traits, is, pleiotropic, will impose larger costs than affect fewer traits. Here we present a systems approach test this expectation. Previous studies have independently estimated and morphological effects of deleting all nonessential genes in Saccharomyces cerevisiae. Using datasets...
The transition from generalist to specialist may entail the loss of unused traits or abilities, resulting in narrow niche breadth. Here we examine process specialization digital organisms--self-replicating computer programs that mutate, adapt, and evolve. Digital organisms obtain energy by performing computations with numbers they input their environment. We examined evolutionary trajectory an ecologically environment, where only a single computation yielded energy. determined extent which...
Abstract Reproductive division of labour is common in many societies, including those eusocial insects, cooperatively breeding vertebrates, and most forms multicellularity. However, conflict over what best for the individual vs. group can prevent an optimal from being achieved. In social amoeba Dictyostelium discoideum , cells aggregate to become multicellular a fraction behaves altruistically, forming dead stalk that supports rest. Theory suggests intra‐organismal spore–stalk cell fate...
Phagocytes are cells that pursue, engulf and kill bacteria. They include macrophages neutrophils of the mammalian immune system, as well free-living amoebae hunt bacteria for food. Phagocytosis can result in diverse outcomes, ranging from sustenance to infection colonization by either pathogens or beneficial symbionts-and thus, discrimination may be necessary seek out good while avoiding bad ones. Here we tested whether soil amoeba Dictyostelium discoideum discriminate among different types...
Micromutational models of adaptation have placed considerable weight on antagonistic pleiotropy as a mechanism that prevents mutations large effect from achieving fixation. However, there are few empirical studies the distribution pleiotropic effects, and no examined this for number adaptive mutations. Here we examine form extent associated with beneficial in Escherichia coli. To do so, used collection independently evolved genotypes, each which contains mutation confers increased fitness...
When overlapping sets of genes encode multiple traits, those traits may not be able to evolve independently, resulting in constraints on adaptation. We examined the evolution genetically integrated digital organisms-self-replicating computer programs that mutate, compete, adapt, and a virtual world. assessed whether overlap encoding two - here, ability perform different logic functions constrained also strong opposing selection could separate otherwise entangled allowing them independently...
Abstract Collective phenotypes, which arise from the interactions among individuals, can be important for evolution of higher levels biological organization. However, how a group’s composition determines its collective phenotype remains poorly understood. When starved, cells social amoeba Dictyostelium discoideum cooperate to build multicellular fruiting body, and morphology body is likely advantageous surviving spores. We assessed number strains, as well their genetic geographic...
Abstract Cooperative groups are susceptible to invasion by cheaters that reap the benefits but fail pay costs. Both theory and experimental work have shown cheating can select for counter-adaptations resist cheating. But then why is so common? One key hypothesis trade-offs prevent resistors from taking over, evidence support trade-off model lacking. Here we evolved resistance different tested trade-offs. Improvements against one cheater frequently entailed correlated improvements novel...
Social groups often form dominance hierarchies, and these hierarchies are almost always linear. However, why linear emerge is not well-understood. In the social amoeba Dictyostelium discoideum , cells a multicellular fruiting body when starved, which consists of ball viable spores held aloft by stalk dead cells. genetically mixed (chimeric) bodies, conflicts can arise over equitable sacrifice to stalk, some strains predictably dominate others in spores. Using pairwise mixes that co-occurred...
Abstract Reproductive altruism, where some individuals reproduce and others do not, is considered one of the pinnacles cooperative societies. However, optimal level reproductive altruism likely to depend on inclusive fitness considerations, including relatedness reproducing non-reproducing individuals, as well benefits costs accruing each, respectively. In social amoeba Dictyostelium discoideum , thousands cells aggregate form a multicellular fruiting body. During this process, die, forming...
Abstract Professional phagocytes detect, pursue, engulf, and kill bacteria. While all professional use chemotaxis to locate bacteria, little is known about whether they can discriminate among them, responding preferentially some bacteria over others. Here we examine the of soil amoeba phagocyte Dictyostelium discoideum in assays where amoebae were presented with a paired choice different We observed variation extent which pursue types preferential migration towards Gram-negative...
Abstract Collective phenotypes, which arise from the interactions among individuals, can be important for evolution of higher levels biological organization. However, how a group’s composition determines its collective phenotype remains poorly understood. When starved, cells social amoeba Dictyostelium discoideum cooperate to build multicellular fruiting body, and morphology body is likely advantageous surviving spores. We assessed number strains, as well their genetic geographic...