Phylogenetics and Diversification of Sailfin and Shortfin Mollies (Mollienesia, Poecilia, Poeciliidae)

Phylogeography aims to understand the formation of species across space and time. Freshwater fishes are studied because they strongly reflect historical and ecological changes in a region. The objective of this dissertation is to identify historic geological events and ecological factors that shaped the evolution of species in the subgenus Mollienesia (Poecilia, Mollienesia, Poeciilidae) within the geologically dynamic regions of Mexico, Central America, and the Caribbean. I investigate the evolutionary relationships in 19 of the 25 species by conducting phylogenetic, species trees with molecular clock estimates, and ancestral area estimates analyses on a multi-locus dataset. The phylogenetic and species trees results support three main groups: Poeciia latipinna, P. sphenops, and P. mexicana species complexes. The molecular clock estimates are inconclusive and ancestral area estimates indicate the diversity originated from the Maya and Chortis blocks. These findings uncover allopatric and ecological speciation events in the three main regions. I also analyze a threegene dataset of fine scale sampling in Mexico of the P. sphenops and P. mexicana species complexes under phylogenetic and haplotype network. The phylogenetic results show that Mexican species are a result of independent invasions from Middle America with subsequent diversification. Haplotype network analyses demonstrate that within species, physiographic barriers or river basins cause strong phylogeographic structure of some species, while others show only weak structuring. These patterns are shared with other Neotropical freshwater fishes, mammals, amphibians, and birds. Lastly, I report on the phylogenetic, population genetics, and geometric morphometrics assessment of the sulfide spring rediscovered species Poecilia thermalis from Mexico, after 150 years of the type locality being unknown to science. Phylogenetic analysis finds P. thermalis to be sister to one population of P. sulphuraria and not an independent lineage, complicating the systematics. Population genetic analyses shows P. thermalis to be genetically distinct from adjacent species found in freshwater and shape analyses finds unique morphological characteristics like an enlarged head and wide mouth to aid in the uptake of oxygen, a limited resource in an extreme habitat. This dissertation identified mechanisms of speciation in the subgenus Mollienesia and contributed a wealth of genetic information from previously unsampled regions

Environmental DNA as a Tool For Assessing Microbial Diversity & Ecological Impacts by Contaminants at a Brownfield Site in Southern California

Brownfield sites are properties with the presence of hazardous substances, toxicpollutants, or contaminants. Based on environmental regulations, these abandoned sitesare considered non-usable due to the presence of a high level of organic and inorganictoxic chemicals. Revitalization of Brownfield sites has ecological, economical and publichealth implications for the local communities. Our designated Brownfield site is locatedon the southern California Central groundwater basin and approximately 8 miles east ofthe Los Angeles River, and was previously used as a steel mill and more recently as a gasstation. In this study, our goal is to provide a baseline for the microbial community inassociation to the presence of heavy metals and toxic volatile chemical leaks resultingfrom previous activities. We employed the environmental DNA (eDNA) metabarcodingapproach on soil samples collected from the site at different depths and transects toprovide a profile of microbial communities directly associated with toxic hazardousmaterials. The bacterial soil composition analysis shows the overall bacterial compositionof the site is altered compared to control; with the class of Acidobacteria being moreabundant in the core and depth soil samples. This class of bacteria can tolerate highlyacidic and heavy metal-containing soils. The identification of bacterial mixture can be agateway to classifying microorganisms that consume or breakdown environmentalpollutants and could be used for future bioremediation purposes

Environmental DNA as a Tool For Assessing Microbial Diversity & Ecological Impacts by Contaminants at a Brownfield Site in Southern California

Brownfield sites are properties with the presence of hazardous substances, toxicpollutants, or contaminants. Based on environmental regulations, these abandoned sitesare considered non-usable due to the presence of a high level of organic and inorganictoxic chemicals. Revitalization of Brownfield sites has ecological, economical and publichealth implications for the local communities. Our designated Brownfield site is locatedon the southern California Central groundwater basin and approximately 8 miles east ofthe Los Angeles River, and was previously used as a steel mill and more recently as a gasstation. In this study, our goal is to provide a baseline for the microbial community inassociation to the presence of heavy metals and toxic volatile chemical leaks resultingfrom previous activities. We employed the environmental DNA (eDNA) metabarcodingapproach on soil samples collected from the site at different depths and transects toprovide a profile of microbial communities directly associated with toxic hazardousmaterials. The bacterial soil composition analysis shows the overall bacterial compositionof the site is altered compared to control; with the class of Acidobacteria being moreabundant in the core and depth soil samples. This class of bacteria can tolerate highlyacidic and heavy metal-containing soils. The identification of bacterial mixture can be agateway to classifying microorganisms that consume or breakdown environmentalpollutants and could be used for future bioremediation purposes

Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California

Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life

The CALeDNA program: Citizen scientists and researchers inventory California’s biodiversity

Climate change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California’s biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire