DOI: 10.5061/dryad.q878c
title: Data from: Variation in opsin genes correlates with signaling ecology in North American fireflies

description: Genes underlying signal reception should evolve to maximize signal
 detection in a particular environment. In animals, opsins, the protein
 component of visual pigments, are predicted to evolve according to this
 expectation. Fireflies are known for their bioluminescent mating signals.
 The eyes of nocturnal species are expected to maximize the detection of
 conspecific signal colours emitted in the typical low-light environment.
 This is not expected for species that have transitioned to diurnal
 activity in bright daytime environments. Here, we test the hypothesis that
 opsin gene sequence plays a role in modifying firefly eye spectral
 sensitivity. We use genome and transcriptome sequencing in four firefly
 species, transcriptome sequencing in six additional species and targeted
 gene sequencing in 28 other species to identify all opsin genes present in
 North American fireflies and to elucidate amino acid sites under positive
 selection. We also determine whether amino acid substitutions in opsins
 are linked to evolutionary changes in signal mode, signal colour and light
 environment. We find only two opsins, one long wavelength and one
 ultraviolet, in all firefly species and identify 25 candidate sites that
 may be involved in determining spectral sensitivity. In addition, we find
 elevated rates of evolution at transitions to diurnal activity, and
 changes in selective constraint on long wavelength opsin associated with
 changes in light environment. Our results suggest that changes in eye
 spectral sensitivity are at least partially due to opsin sequence.
 Fireflies continue to be a promising system in which to investigate the
 evolution of signals, receptors and signalling environments.
description: LW opsin nucleotide
 alignmentLong-wavelength opsin
 nucleotide sequence alignment for 38 North American firefly species (FASTA
 format).LW_38tax_formatted.fastaLW opsin amino acid alignmentLong-wavelength opsin amino acid sequence alignment for 38 North American firefly species (FASTA format).LW_38_aa_formatted.fastaUV opsin nucleotide alignmentUltraviolet opsin nucleotide sequence alignment for 38 North American firefly taxa (FASTA format).UV_38_formatted.fastaUV opsin amino acid alignmentUltraviolet opsin amino acid sequence alignment for 38 North American firefly species (FASTA format).UV_38aa_formatted.fastaTree 1 (Stanger-Hall and Lloyd taxa + 14 taxa)BEAST phylogeny constructed with taxa from Stanger-Hall and Lloyd (2015) plus 14 additional taxa. The tree has been trimmed to include only species used in this study.BEAST_SL2015_plus14tax.treTree 2 (Stanger-Hall and Lloyd taxa plus 32 taxa)BEAST phylogeny constructed with taxa from Stanger-Hall and Lloyd (2015) plus 32 additional taxa. The tree has been trimmed to include only species used in this study. Its topology, presented in Text S3, differs slightly from Tree 1, which is presented in the main text.BEAST_SL2015_plus32tax.treTranscriptome_assembliesA zipped folder containing assembled transcriptomes for all 10 species used in this study. After qc, reads were assembled using Trinity with default parameters. These files give the resulting contigs in FASTA format. See README for more details.