Hidden diversity in corals and their endosymbionts [electronic resource]

Understanding the ecological and evolutionary processes that are responsible for the origin, distribution and maintenance of biodiversity is integral to interpreting the dynamics of natural systems and has important implications for a large number of disciplines including epidemiology, agriculture and biodiversity conservation. In this dissertation, I use genetic data to explore the evolutionary histories of two members of the coral holobiont, the coral host and its photosynthetic endosymbionts, which together form the structural foundation of the ocean's most diverse ecosystems. First, I focus on the coral host and explore the evolutionary histories of four closely related species within the abundant and diverse genus, Acropora. In Chapter 1, I utilize multi-locus population genetics to quantitatively test several alternative hypotheses for the high levels of shared genetic variability among species, and I demonstrate that these evolutionary patterns can largely be explained through a combination of a) morphologically cryptic species complexes and b) historical and/or contemporary genetic exchange among species (introgression). Then, in Chapter 2, I explore the geographic distribution of these morphologically cryptic species complexes and examine the consistency of introgression across space. I show that a) there are a handful of geographically widespread, morphologically cryptic species within each species complex, b) there is considerable overlap in the geographic ranges of the cryptic species and c) patterns of introgression are consistent throughout sympatric distributions. Second, I examine the evolutionary diversity of the photosynthetic dinoflagellates that form symbioses with these corals (Symbiodinium), a partnership that is integral for the health of coral reefs. I explore diversity within this group at two distinct taxonomic levels. In Chapter 3, I investigate patterns of nucleotide substitution among deeply divergent clades of Symbiodinium to highlight specific genes and functional groups that may be involved in adaptation of clade D Symbiodinium to high temperature environments, including a fatty acid desaturase, several chaperones and genes involved in photosynthesis and the thylakoid membrane. Then, in Chapter 4, I utilize high throughput transcriptome sequence data to provide an initial look at population-level diversity within two divergent subclades of Symbiodinium. My results illustrate unexpectedly high levels of polymorphism within each of these subclades, and demonstrate that the distribution of these polymorphisms, within and between corals, suggests that they primarily originate from intragenomic variation in multi-copy gene families. Combined, this work illustrates the evolutionary complexity of reef corals and their endosymbionts. A thorough understanding of these complexities is necessary in order to properly address questions regarding the ecological function and resilience of these economically important ecosystem builders.

Keywords: Biology.
Advisor: Palumbi Stephen R. primary advisor. Thesis advisor
Hadly Elizabeth Anne
Petrov Dmitri Alex