RECONSTRUCTING THE EVOLUTIONARY HISTORY OF DARTERS (PERCIDAE: ETHEOSTOMATINAE): EPIGENETIC DIVERGENCE AS A FIRST STEP IN SPECIATION
Creators: name: Smith, Tracy
Publisher: name: Maryland Shared Open Access Repository
Year: 2014
Subjects: AFLP
Darters
MSAP
Population Epigenetics
Speciation

description: This doctoral research reconstructs the evolutionary history and investigates the possibility of changes in gene expression, rather than nucleotide sequence, being a first step in speciation in the second most speciose group of freshwater fishes in North America. To gain a better understanding of the incredible diversity in this group of fishes known as darters (Percidae: Etheostomatinae), I first determine evolutionary relationships among 69 and then 101 different species representing four genera of darters using a genome-scan approach known as AFLP. Prior to this work, AFLPs had only been used for recent divergences, with the oldest reconstruction dating to approximately 15 million years. In silico studies had predicted that increased homoplasy would weaken the utility of AFLPs in reconstructing ancient evolutionary relationships. We found that dense taxon sampling increased accuracy and resolution in this group of fishes. We were able to resolve problematic nodes and reconstruct the evolutionary history of darters with moderate to strong statistical support at ancient divergences (&gt;25 mya) and thus champion this method for deeper relationships. In addition, we were able to propose a new taxonomic classification of darters based on our and other recent phylogenies.  Phylogenetic reconstruction revealed a large amount of interspecific genetic diversity in this group of fishes. This finding led us to question whether fast-evolving changes in gene expression via changes to the methylome, rather than nucleotide sequence, could initiate speciation in this group of fishes. We investigated whether epigenetic divergence acts as a first step in speciation in &lt;italic&gt;Etheostoma&lt;/italic&gt;, a genus of darters. Using Methyl-Sensitive Amplified Polymorphisms (MSAP), we analyzed population structure and differentiation in the methylome and genome across 5 populations of &lt;italic&gt;E. olmstedi&lt;/italic&gt; (the tessellated darter) in the Patuxent River and 6 populations in the Potomac River in Maryland, USA. We predicted that epigenetic variation would be greater than genetic variation both within and between populations, with populations showing greater differentiation in their methylomes compared to their genomes. We also investigated the relationship between genetic divergence, epigenetic divergence, and the strength of various reproductive barriers across more distantly related, geographically isolated species in the subgenera &lt;italic&gt;Ulocentra, Etheostoma&lt;/italic&gt; and &lt;italic&gt;Nanostoma&lt;/italic&gt;. Since previous studies have shown behavioral isolation to be the strongest reproductive barrier between darter species, we predicted that behavioral isolation would be better predicted by epigenetic as compared to genetic differences. Our results indicate that the methylome is indeed changing faster than the nucleotide sequence across all levels of divergence, and that epigenetic divergence better predicts behavioral reproductive isolation than genetic divergence, supporting the hypothesis that epigenetic divergence can act as a first step in speciation in this group.