Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation


Arts and Sciences



First Advisor

Dr. David W. Weisrock


Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns that exist in natural systems by generating robust estimates of the underlying species history, quantify support for alternative hypotheses of lineage formation, and describe patterns of genetic variation present in robust nuclear genomic datasets. Empirically testing correlations between mitonuclear genomic conflict and reduced gene flow at the organism level will contribute toward a better understanding of lineage boundaries and how intergenomic interactions shape the process of divergence.

Mitochondrial introgression has been inferred in many salamander systems with limited perspective from nuclear sequence data. Within dusky salamanders (Desmognathus), these patterns have been observed between morphologically and geographically disparate populations. I sequenced regions throughout the nuclear genome to reconstruct species trees, performed population-level analyses testing concordance between the mitochondrial, nuclear datasets, and nuclear genes with mitochondrial functions with the expectation that coevolutionary interactions among genomes are more likely to manifest in these regions. I also estimated migration rates between populations that may have experienced historical mitochondrial introgression to evaluate phylogeographic patterns.

Using these data we definitively reject species models in which genetic boundaries are based solely on mitochondrial data, favoring geographic models instead. Furthermore, analyses soundly reject current taxonomic models based on morphological characteristics, suggesting there is greater lineage diversity than is currently recognized.

I also used empirical assays of pre-zygotic reproductive mating behavior within and among populations containing diverse mitochondrial lineages to test metrics of reproductive isolation, and to determine if introgression shapes the evolution of complex traits directly influencing rates of divergence. These results may explain incongruent patterns observed between the mitochondrial and nuclear data as a function of inheritance and population dynamics rather than directly functioning to suppress nuclear gene flow.

This research builds upon recent studies suggesting that speciation is a highly complex and often non-bifurcating process in which introgression can have a profound and lasting signature on the nuclear evolutionary history. Mechanisms responsible for divergence with gene flow challenge evolutionary biologists to reevaluate our notions and definitions of species boundaries to accommodate seemingly conflicted genomic patterns within and between genomes.

Digital Object Identifier (DOI)