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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Thesis
  • Peer Reviewed
UC Merced Electronic Theses and Dissertations (2012)

Patterns of dispersal and gene-flow in freshwater invertebrates have often been difficult to interpret. Despite the assumed high potential for dispersal, populations of freshwater invertebrates display high genetic differentiation over small distances. There have been several explanations posed for this gene flow dispersal paradox, including strong priority effects or low realized dispersal. This study explores the spatial genetic structure of the freshwater invertebrate Branchinecta lynchi, a threatened vernal pool inhabitant, at two scales with a goal to determine the scale at which gene flow is important in shaping these patterns. Vernal pools were sampled at two different localities the San Luis National Wildlife Refuge Complex and a preserve adjacent to the University of California, Merced. Individuals were genotyped using both the mitochondrial cytochrome oxidase I subunit (COI) and nuclear amplified fragment length polymorphisms (AFLPs). Pairwise Fst values showed that genetic structure for this species was high, however, the only geographic pattern that emerged was isolation by distance at the local scale for the COI marker. Discrepancies between mitochondrial and AFLP markers may be explained several ways, including genotyping error, sex-biased dispersal and/or the longer time to equilibrium of the nuclear genome. These results suggest that gene flow is important at the local scale, at least for mitochondrial DNA, while historical colonization patterns are likely maintained at the regional scale by priority effects. I infer that maintaining connectivity among vernal pool complexes through local dispersal vectors should be a management priority.

    Cover page: Population structure of the vernal pool fairy shrimp (Branchinecta lynchi) at two spatial scales
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2015)
    Background: The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates. Results: We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3' and 5' UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions. Conclusions: We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.
      Cover page: Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes)
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