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

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 (Sergia and Sergestes) 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 -sergestes group was
rendered non-monophyletic, and the -sergia 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 -sergia group, but were
later lost in the deepest living genus, Sergia.  Lensed
photophores also evolved once within the genera Prehensilosergia,
Lucensosersgia, and Challengerosergia.  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.