.............................................................................................................................................................. 5 Introduction ........................................................................................................................................................ 6 Methods ............................................................................................................................................................. 10 Results ............................................................................................................................................................... 18 Discussion ......................................................................................................................................................... 26 Acknowledgements ......................................................................................................................................... 33 References......................................................................................................................................................... 34 Table of Figures and Tables Figure 1: Phylogenetic tree of Strongylocentrotid urchins showing the six-focal species as well as well as their general distribution, and their preferred depth: Deep, Moderate, or Shallow. The distribution of species is abbreviated as NWP and NEP for Western and Eastern Pacific, and CIR for Circumpolar, which means species are in the Artic as well as the NE and NW Pacific. A. is Allocentrotus H. is Hemicentrotus, and P is Pseudocentrotus. Note species names have not yet been changed to reflect phylogenetic findings. From Kober and Pogson 2017. .................................... 8 Figure 2: Flow chart showing the different stages of the introgression detection pipeline pioneered in this study. ..................................................................................................................................................... 10 Figure 3: Direction and magnitude of detected introgression events. Introgression events with more than eight genes have bolded counts for clarity. Arrows to scale by width. ............................. 18 Figure 4: Sp-Z59 has conflicting genetic histories in different exons that obscured introgression at the whole genes level and resulted in the recovering of a whole gene tree with a different topology. ........................................................................................................................................................... 22 Figure 5: Sp-CholdhL has conflicting genetic histories that result in reduced bootstrap support for the introgression topology in the whole gene tree.................................................................................... 23 Figure 6: Many Introgressed Sites are Non-Synonymous ....................................................................... 24 Figure 7: Verified Introgression events plotted by species pair ............................................................. 25 -----------------------Table 1: The relative performance of each initial identification test and combination thereof from identification to quantification of introgression. Note: Not all VI genes had ABBA-BABA testable topologies. ......................................................................................................................................................... 18 Table 2: Ranked Wilcox Test Results of the K2PDs of VI genes against the full data set. Significant results bolded. .............................................................................................................................. 19 Quantifying Adaptive Introgression in Strongylocentrotid Urchins Kan 4 Table 3: Gene Ontology Term Enrichment and Under-Enrichment for Verified Introgression Genes. Membrane and receptor related categories in italics. P-values corrected for a FDR of 0.05. ............................................................................................................................................................................ 21 Quantifying Adaptive Introgression in Strongylocentrotid Urchins Kan 5