DOI: 10.5061/dryad.vdncjsxvk
title: Sergestidae shrimp family single- and multi-gene alignments and tree files

description: 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. 
description: PHYLOGENETIC TREE CONSTRUCTION 
 Specimens were collected via mid-water trawls in the Gulf of
 Mexico and Florida Straits.  Abdominal muscle tissue
 was removed from the specimens for genomic DNA extraction using either
 Qiagen DNEasy Blood and Tissue Kits or a Phenol Chloroform
 protocol.   PCR protocols were employed to target H3,
 NaK, COI, and 16S for Sanger sequencing.  PCR
 products were sequenced through the company Genewiz in Boston, MA,
 USA. Genome skimming was
 employed to extract entire mitochondrial genomes.  
 Extracted genomic DNA was first sonicated to achieve chromosomal
 fragmentation of ~200 bps.   Libraries were prepared
 using NEB Next Ultra II Library Prep kits. Libraries
 were sequenced through the company Genewiz in Boston, MA, USA on an
 Illumina HiSeq 3000/4000. Raw NGS sequence data was
 assembled into complete mitochondrial genomes with NOVOplasty assembling
 tool, using 16s / COI seed sequences of closely related species acquired
 through Sanger sequencing, or published in NCBI's online database,
 Genbank.   Assembled mtGenomes were annotated using
 MITOS online web tool. 
 Genetic sequence data handling, cleaning, and organization was
 conducted using the bioinformatics software, Geneious Prime.  
 Raw Sanger sequence data from Genewiz was assembled, cleaned,
 and trimmed.  NGS sequence data from MITOS annotation was cleaned and
 trimmed Single-gene alignments of Sanger sequencing
 and NGS genes were created using MAFFT alignment tool in
 Geneious. Single-gene trees
 were constructed from Genious alignments using IQTREE phylogenetic
 software to screen for contaminated sequences and genes lacking
 phylogenetic signal. Final single-gene alignments
 were concatenated into single multi-gene alignment using Geneious
 Prime. Final multi-gene trees were constructed from
 multi-gene alignment using IQTREE and MrBayes phylogenetic
 software. ANCESTRAL STATE
 RECONSTRUCTION Multi-gene tree was imported
 to Mesquite software and pruned to include only one individual per
 species. Coding matrix created to assign a number to
 each species depending on light organ type. 0 = Light
 organ absent 1 = Organ of Pesta
 2 = Non-lensed Photophore 3 = Lensed
 Photopore Maximum likelihood
 and maximum parsimony ancestral state reconstruction created in
 Mesquite.