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Open Access Publications from the University of California

Scholarly Works (4 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2023)
The dynamical structure of ecological communities results from interactions among taxa that change with shifts in species composition in space and time. However, our ability to study the interplay of ecological and evolutionary processes on community assembly remains relatively unexplored due to the difficulty of measuring community structure over long temporal scales. Here, we made use of a geological chronosequence across the Hawaiian Islands, representing 50 years to 4.15 million years of ecosystem development, to sample 11 communities of arthropods and their associated plant taxa using semi-quantitative DNA metabarcoding. We then examined how ecological communities changed with community age by calculating quantitative network statistics for bipartite networks of arthropod-plant associations. The average number of interactions per species (linkage density), ratio of plant to arthropod species (vulnerability), and uniformity of energy flow (interaction evenness) increased significantly in concert with community age. The index of specialization H2’ has a curvilinear relationship with community age. Our analyses suggest that younger communities are characterized by fewer but stronger interactions, while biotic associations become more even and diverse as communities mature. These shifts in structure became especially prominent on East Maui (~0.5 my) and older volcanos, after enough time had elapsed for adaptation and specialization to act on populations in situ. Such natural progression of specialization during community assembly is likely impeded by the rapid infiltration of non-native species, with special risk to younger or more recently disturbed communities that are composed of fewer specialized relationships.
    Cover page: Ecological network structure in response to community assembly processes over evolutionary time
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2021)

    Understanding why we find different types and numbers of species in different places has been a long-standing question for biologists. Ecological communities provide a conceptual and literal framework for unraveling generalizations about the composition, distribution, and dynamics of biodiversity. Communities assemble via ecological and evolutionary mechanisms that lead to the accumulation of species and the development of species interactions. Insights into the dynamics of community assembly have relied extensively on theoretical work or studies with limited spatiotemporal scale. Directly studying community structure through time using long-term time-series data offers an exciting opportunity to link evolutionary relatedness across multiple taxa and the ecological attributes of the communities in which they occur, within a dynamic framework. Oceanic archipelagos provide a chance to sample communities from discrete time points during community assembly. Present-day communities face threats, such as climate change and invasive species, demanding more holistic approaches that consider all species in an ecosystem and the interactions between them. Advancements in molecular techniques, bioinformatics, and data science have led to the possibility of a more comprehensive understanding of the structural properties of communities and of biodiversity overall. The research presented here explores the interplay of ecological and evolutionary processes on biodiversity dynamics over deep time. I employ multiple research approaches including field collections, laboratory work with environmental DNA and museum specimens, macroecological theory, and network thinking to create a novel synthesis of information for understanding the evolution of ecological communities. First, I highlight the singular importance of insular systems for studying fundamental questions in ecology and evolutionary biology. By recording patterns of species accumulation and genetic distances in multiple arthropod lineages, I explore patterns of community assembly over time and how they differ between lineages. Additionally, I investigate systematic deviations in observed species abundance distributions from predictions of theory for understanding community steady state. Last, I demonstrate the implications of shifting network architecture metrics for understanding ecosystem change. My work makes critical advances in understanding biodiversity, community assembly, and the consequences of environmental perturbations on ecological communities.

      Cover page: Resolving Ecological, Evolutionary, and Global Change Effects on Biodiversity Dynamics: A Review and Empirical Study
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2019)

      Background

      In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies).

      Findings

      Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates.

      Conclusions

      Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.
        Cover page: Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2023)
        Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.
          Cover page: Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae)
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