Convergent evolution is a ubiquitous phenomenon in the history of life. Classic examples of convergent traits, such as the camera-eyes in vertebrates and cephalopods or the wings of bats, birds and insects, convey the efficacy of natural selection as well as the common environmental constraints shared by organisms. Yet, the extent to which convergent molecular processes accompany structural convergence remains unclear. Convergent forms of bioluminescence have originated often across diverse forms of life, providing an excellent system for investigating the molecular signature of convergent evolution. Within cephalopods, an unusual form of bioluminescence dependent on luminous symbiotic bacteria has evolved multiple times. This project focuses on two distantly related species of squid, Euprymna scolopes and Uroteuthis edulis, which rely on such bioluminescent organs for a form of crypsis called counter-illumination. Although these species are separated by 300 million years of evolution, both organs invariably develop as distinctively bi-lobed structures called photophores, featuring prominent crystalline lenses and reflectors, and can recruit and culture luminous bacteria from surrounding waters.

Here, I develop novel phylogenetic and quantitative approaches that reveal evidence that the evolution of a convergent phenotype is associated with the convergent expression of thousands of genes. To achieve this, I first infer the relationships among extant cephalopods using a multi-gene supermatrix approach for over 400 species. Using a series of independent phylogenetic analyses---including an implementation of a novel continuous-time Markov modeling approach---I then demonstrate that bacterial photophores have originated repeatedly during squid evolution. With this phylogenetic evidence strongly favoring convergence, I then assayed the expression of a suite of genes with documented roles in photophore physiology in a representative species from each of the two clades in which my analysis suggests independent origins. In Euprymna, we know that this complex organ not only regulates bacterial activity and modulates light output but also uses light-sensitive cells to detect light levels. Results of the quantitative expression assays largely concurred with the phylogenetic assessment: many key photophore genes are expressed at different levels between the two species.

However, a different picture emerged upon comparison of global gene expression profiles underlying the two photophores. Using Illumina high-throughput sequencing I recovered full transcriptomes from the photophores as well as homologous traits from the two species. Three different measures of similarity indicate striking similarity between convergent photophores---as similar as expected in homologous traits. To account for possible co-linearity among genes (e.g., genetic modules), I also developed a regression technique to model tissue transcriptomes while minimizing the effect of co-varying gene expression values. These models suggest that not only homologous traits but also the convergent photophores have highly predictable gene expression patterns.

Finally, I quantify and annotate genes specific to photophores in both species to determine which genes of similar function have been co-opted during the evolution of both photophores. Among the transcripts identified with high and/or localized expression in the photophore are several components of the innate immune system. This discovery contributes to the growing body of evidence that the innate immune system plays a crucial role in animal-microbe symbioses. The emerging picture suggests that, while the convergent evolution of bacterial photophores is characterized by a number of differences in gene expression---evident in candidate gene assays, the transcriptomic landscapes underlying these traits are largely congruent. Thus, squid bacterial photophores provide evidence that congruent expression patterns of thousands of genes can mirror the phenotypic evolution of a convergent trait.