Patterns and Processes of Speciation and Phenotypic Diversification in Palm-Pitvipers (Viperidae: \u3ci\u3eBothriechis\u3c/i\u3e)

Diversification is primarily a function of two processes—speciation and adaptation—that shape the history and trajectory of evolutionary lineages. These processes are often interdependent and are shaped by biotic and abiotic factors including existing and evolvable genetic variation, selection, and genetic connectivity among lineages. Genomic datasets present a means of disentangling complex evolutionary signals by sampling hundreds or thousands of loci to interrogate lineage and/or trait diversification. Palm-pitvipers (Bothriechis) are well suited for testing evolutionary hypotheses related to speciation and adaption. This group of arboreal vipers is well-recognized as monophyletic with a contentious phylogeographic history. Moreover, these species’ venoms are an ideal adaptive trait for examining genotype-phenotype interactions. To understand the processes affecting speciation in palm-pitvipers, I estimated the group’s phylogeny using an anchored phylogenomics approach and tested for evidence of reticulate evolution (i.e., ancient gene-flow) in the group\u27s history. The recovered phylogeny conflicted with key relationships inferred by mitochondrial genes and tests for reticulate evolution revealed strong support for historic gene flow among geographically proximate lineages. To examine the mechanisms promoting macroevolutionary divergence of venom phenotypes, I first focused on two sister taxa with strongly divergent venom types: The Black-Speckled (B. nigroviridis) and Talamancan (B. nubestris) Palm-Pitvipers. I tested whether toxins underlying venom differentiation would be associated with modular transcript expression. I found that toxins responsible for specific phenotypes segregate into distinct co-expression modules, which may permit rapid differentiation of venoms. To expand my investigation, I assembled venom gland transcriptomes from all recognized species of palm-pitvipers and assessed how gene family evolution affected patterns of toxin expression. Toxin expression was highly variable within toxin families but more variable following speciation events than gene duplications. Additionally, I identified multiple lineage specific regimes of expression for specific PLA2 and SVMP genes. Despite the broad expression variation characteristic of toxin genes, lineage-specific patterns of toxin expression emphasize the effect of shared evolutionary history on underlying genetic architecture. More broadly, the complexities of speciation and venom phenotype evolution observed in palm-pitvipers demonstrate the variety of processes that can influence evolutionary trajectories