Dissertations, Theses, and Capstone Projects

Date of Degree

2-2019

Document Type

Dissertation

Degree Name

Ph.D.

Program

Biology

Advisor

Kenneth G. Karol

Committee Members

José D. Anadón

Michael J. Hickerson

Richard M. McCourt

John D. Wehr

Subject Categories

Biodiversity | Bioinformatics | Biology | Botany | Genomics | Plant Biology | Terrestrial and Aquatic Ecology

Keywords

algae, starry stonewort, freshwater

Abstract

Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and serve important roles in stabilizing sediment, sequestering nutrients, and providing forage for fish and waterfowl. Although most Characeae are considered beneficial in freshwater ecosystems, one species, Nitellopsis obtusa (Desv. in Loisel.) J. Groves, has been identified as an invasive species in North America. In the first research chapter (Chapter 2) a systematic survey of 390 sites across New York state was conducted to discover new populations of Nitellopsis obtusa and confirm the known distribution of this invasive species. In the third chapter the survey was extended to include New England, for a total of 740 sites, from which species distribution models were constructed. These models demonstrated that water chemistry variables can predict Characeae habitat, and that species can be classified as specialist species, occurring in a narrow chemical niche, while others can be classified as generalist species that occur broadly across the region. Scenarios simulating increased nutrient pollution and future climate change were explored with some species predicted to increase in range and other species predicted to be extirpated from the region. Nitellopsis obtusa was found to be a hard water specialist, occurring at sites with elevated levels of calcium. Models found the niche of Nitellopsis obtusa similar to Chara contraria, a native species whose distribution can be used to identify sites that may be susceptible to Nitellopsis obtusa invasion. In the fourth chapter the fully sequenced and annotated organellar genomes of Nitellopsis obtusa are presented with an analysis of the genetic patterns of invasion. The chloroplast genome was more variable than the mitochondrial genome, and both genomes showed that samples in the invasive range were nearly identical, evidence of a single introduction event. Invasive samples clustered most closely but were not identical to samples from Western Europe, specifically France. Intra-individual polymorphism of the mitochondrial genome was detected and PacBio sequencing indicated that polymorphism likely arises from transfer of mitochondrial regions to the nuclear genome. In the fifth chapter a draft nuclear genome of Nitellopsis obtusa is presented and used to determine whether rapid adaptation in the invasive range gave rise to a more successful invasive genotype. The genome of Nitellopsis obtusa was estimated by kmer counting to be 2.5-5 Gb. A highly fragmented assembly of 2.3Gb was achieved. Double digest restriction site associated DNA sequencing (ddRAD) of individuals across the native and invasive range was unable to detect a signal of differentiation in putative adaptive genes, possibly due to cross-contamination during the pooling step of library construction. The results of these studies provide insights relevant for freshwater conservation and invasive species outreach and management.

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