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Open Access Publications from the University of California

Scholarly Works (19 results)

  • Article
  • Peer Reviewed
Papers (2007)

To understand the complex interactions among animals within an ecosystem, biologists need to be able to track their location and social interactions. There are a variety of factors that make this difficult. We propose using adaptive, embedded networked sensing technologies to develop an efficient means for wildlife monitoring. This paper surveys our research; we demonstrate how a self-organizing system can efficiently conduct real-time acoustic source detection and localization using distributed embedded devices.

    Cover page: Automated Wildlife Monitoring Using Self-Configuring Sensor Networks Deployed in Natural Habitats
    • Article
    Papers (2003)

    Communication among adaptive agents can be framed as language acquisition and broken down into three problems; symbol grounding, language learning, and language evolution. We propose that this view clarifies many of the difficulties framing issues of collaboration and self-organization. Additionally, we demonstrate simple classification systems that can provide the first step in grounding real-world data and provide general schema for constructing other such systems. The first system classifies auditory input from frog calls and is presented as a model of grounding objects. The second system uses the minimum description length framework to distinguish patterns of robot movement as a model of grounding actions.

      Cover page: Adaptive Communication among Collaborative Agents: Preliminary Results from Symbol Grounding
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)

      Background

      Rapid adaptation to new environments can facilitate species invasions and range expansions. Understanding the mechanisms of adaptation used by invasive disease vectors in new regions has key implications for mitigating the prevalence and spread of vector-borne disease, although they remain relatively unexplored.

      Results

      Here, we integrate whole-genome sequencing data from 96 Aedes aegypti mosquitoes collected from various sites in southern and central California with 25 annual topo-climate variables to investigate genome-wide signals of local adaptation among populations. Patterns of population structure, as inferred using principal components and admixture analysis, were consistent with three genetic clusters. Using various landscape genomics approaches, which all remove the confounding effects of shared ancestry on correlations between genetic and environmental variation, we identified 112 genes showing strong signals of local environmental adaptation associated with one or more topo-climate factors. Some of them have known effects in climate adaptation, such as heat-shock proteins, which shows selective sweep and recent positive selection acting on these genomic regions.

      Conclusions

      Our results provide a genome wide perspective on the distribution of adaptive loci and lay the foundation for future work to understand how environmental adaptation in Ae. aegypti impacts the arboviral disease landscape and how such adaptation could help or hinder efforts at population control.
        Cover page: Genomic signatures of local adaptation in recent invasive Aedes aegypti populations in California.
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2021)
        Cas9/guide RNA (gRNA)-based gene drive systems are expected to play a transformative role in malaria elimination efforts., whether through population modification, in which the drive system contains parasite-refractory genes, or population suppression, in which the drive system induces a severe fitness load resulting in population decline or extinction. DNA sequence polymorphisms representing alternate alleles at gRNA target sites may confer a drive-resistant phenotype in individuals carrying them. Modeling predicts that, for observed levels of SGV at potential target sites and observed rates of de novo DRA formation, population modification strategies are uniquely resilient to DRAs. We conclude that gene drives can succeed when fitness costs incurred by drive-carrying mosquitoes are low enough to prevent strong positive selection for DRAs produced de novo or as part of the SGV and that population modification strategies are less prone to failure due to drive resistance.
          Cover page: Population modification strategies for malaria vector control are uniquely resilient to observed levels of gene drive resistance alleles.
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2020)
          A number of recent papers report that standing genetic variation in natural populations includes ubiquitous polymorphisms within target sites for Cas9-based gene drive (CGD) and that these "drive resistant alleles" (DRA) preclude the successful application of CGD for managing these populations. Here we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that ~90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of ≥1.0%. We conclude that the abundance of conserved target sites in mosquito genomes and the inherent flexibility in CGD design obviates the concern that DRAs present in the standing genetic variation of mosquito populations will be detrimental to the deployment of this technology for population modification strategies.
            Cover page: Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2015)
            Animal species adapt to changes in their environment, including man-made changes such as the introduction of insecticides, through selection for advantageous genes already present in populations or newly arisen through mutation. A possible alternative mechanism is the acquisition of adaptive genes from related species via a process known as adaptive introgression. Differing levels of insecticide resistance between two African malaria vectors, Anopheles coluzzii and Anopheles gambiae, have been attributed to assortative mating between the two species. In a previous study, we reported two bouts of hybridization observed in the town of Selinkenyi, Mali in 2002 and 2006. These hybridization events did not appear to be directly associated with insecticide-resistance genes. We demonstrate that during a brief breakdown in assortative mating in 2006, A. coluzzii inherited the entire A. gambiae-associated 2L divergence island, which includes a suite of insecticide-resistance alleles. In this case, introgression was coincident with the start of a major insecticide-treated bed net distribution campaign in Mali. This suggests that insecticide exposure altered the fitness landscape, favoring the survival of A. coluzzii/A. gambiae hybrids, and provided selection pressure that swept the 2L divergence island through A. coluzzii populations in Mali. We propose that the work described herein presents a unique description of the temporal dynamics of adaptive introgression in an animal species and represents a mechanism for the rapid evolution of insecticide resistance in this important vector of human malaria in Africa.
              Cover page: Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets
              • Article
              Papers (2003)

              This paper describes a framework for studies of the adaptive acquisition and evolution of language, with the following components: language learning begins by associating words with cognitively salient representations (“grounding”); the sentences of each language are determined by properties of lexical items, and so only these need to be transmitted by learning; the learnable languages allow multiple agreements, multiple crossing agreements, and reduplication, as mildly context sensitive and human languages do; infinitely many different languages are learnable; many of the learnable languages include infinitely many sentences; in each language, inferential processes can be defined over succinct representations of the derivations themselves; the languages can be extended by innovative responses to communicative demands. Preliminary analytic results and a robotic implementation are described.

                Cover page: The Learning and Emergence of Mildly Context Sensitive Language
                • Article
                Papers (2003)
                  Cover page: Grounding as Learning
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2018)
                  Here we report the complete mitochondrial sequences of 70 individual field collected mosquito specimens from throughout Sub-Saharan Africa. We generated this dataset to identify species specific markers for the following Anopheles species and chromosomal forms: An. arabiensis, An. coluzzii (The Forest and Mopti chromosomal forms) and An. gambiae (The Bamako and Savannah chromosomal forms).  The raw Illumina sequencing reads were mapped to the NC_002084 reference mitogenome sequence. A total of 783 single nucleotide polymorphisms (SNPs) were detected on the mitochondrial genome, of which 460 are singletons (58.7%). None of these SNPs are suitable as molecular markers to distinguish among An. arabiensis, An. coluzzii and An. gambiae or any of the chromosomal forms. The lack of species or chromosomal form specific markers is also reflected in the constructed phylogenetic tree, which shows no clear division among the operational taxonomic units considered here.
                    Cover page: Mitochondrial genomes of <i>Anopheles arabiensis</i>, <i>An. gambiae</i> and <i>An. coluzzii</i> show no clear species division.
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2021)
                    Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome study of 142 specimens from nine countries in continental Africa and three islands in the Gulf of Guinea. This sample set covers a large part of this species' geographic range. Our population genomic analyses included a description of the structure of mainland populations, island populations, and connectivity between them. Three genetic clusters are identified among mainland populations and genetic distances (FST) fits an isolation-by-distance model. Genomic analyses are applied to estimate the demographic history and ancestry for each island. Taken together with the unique biogeography and history of human occupation for each island, they present a coherent explanation underlying levels of genetic isolation between mainland and island populations. We discuss the relationship of our findings to the suitability of São Tomé and Príncipe islands as candidate sites for potential field trials of genetic-based malaria control strategies.
                      Cover page: The origin of island populations of the African malaria mosquito, Anopheles coluzzii
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