Sergestidae shrimp family single- and multi-gene alignments and tree files

<p>Deep-sea shrimp belonging to the family Sergestidae provide a unique system for studying the evolution of bioluminescence.  Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores, non-lensed photophores, or internal organs of Pesta.  This morphological diversity across Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (<em>Sergia </em>and<em> Sergestes</em>) into 15.  Here, we capitalize on molecular data to construct an updated genus-level phylogeny of sergestid shrimp.  DNA was successfully extracted from approximately 87 individuals belonging to 13 of the 15 newly proposed genera.  We implemented a "genome skimming" approach, allowing us to capture mitochondrial genomic data across 19 Sergestidae species.  Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3, NAK) and mitochondrial (16S and COI) genes.  The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships.  The -<em>sergestes</em> group was rendered non-monophyletic, and the -<em>sergia</em> group was recovered as monophyletic.  Ancestral state reconstructions of light organ type indicate the organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -<em>sergia</em> group, but were later lost in the deepest living genus, <em>Sergia</em>.  Lensed photophores also evolved once within the genera <em>Prehensilosergia</em>, <em>Lucensosersgia</em>, and <em>Challengerosergia</em>.  Our findings identify preliminary patterns across light organ type and species' depth distributions, however future research that incorporates finer-scale depth data and more species is needed to confirm our findings. </p>