10.5061/DRYAD.737C8T8
Martin, Gavin
Brigham Young University
Stanger-Hall, Kathrin
University of Georgia
Branham, Marc
University of Florida
Da Silveira, Luiz
University of Georgia
Lower, Sarah
Bucknell University
Hall, David
University of Georgia
Li, Xue-Yan
Chinese Academy of Sciences
Lemmon, Alan
Florida State University
Lemmon, Emily
Florida State University
Bybee, Seth
Brigham Young University
Data from: Higher-level phylogeny and reclassification of Lampyridae
(Coleoptera: Elateroidea)
Dryad
dataset
2020
Molecular systematics
Lampyridae
National Science Foundation
https://ror.org/021nxhr62
DEB-1655981
2020-10-31T00:00:00Z
2019-12-17T00:00:00Z
en
https://doi.org/10.1093/isd/ixz024
219060577 bytes
5
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Fireflies (Lampyridae) are a diverse family of beetles which exhibit an
array of morphologies including varying antennal and photic organ
morphologies. Due in part to their morphological diversity, the
classification within the Lampyridae has long been in flux. Here we use an
anchored hybrid enrichment approach to reconstruct the most extensive
molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and to
evaluate firefly higher-level classification. We propose several
classification changes supported by morphological evidence: (1)
Lamprigera, Vestini (incl. Vesta, Dodacles, Dryptelytra, and Ledocas),
Photoctus, and Araucariocladus are transferred to Lampyridae incertae
sedis, (2) Phausinae subfamilia nova is erected for Phausis and
Lamprohiza, (3) Psilocladinae status nova is reestablished for the genus
Psilocladus, (4) Pollaclasis is transferred to the Cyphonocerinae, (5)
Memoan is transferred to Amydetinae, and (6) Scissicauda is transferred to
Lampyrinae.
Full Alignment The sequences obtained for individual loci were aligned via
Mafft v. 7.407 (Katoh and Standley 2013) using the default automatic
alignment option. For Maximum Likelihood (ML) analyses, the alignments of
the individual loci included flanking regions (head, tail, or both) of
each locus and were concatenated before analysis and resulted in an
alignment length of 1,833,533 base pairs. Lampyridae_align.fasta Cleaned
Alignment file Breinholt et al. (2017) showed that trimming data from the
probe or flanking region has little effect on the final topology,
consequently, we elected not to trim these regions (Lemmon et. al. 2012).
However, it is possible that missing data may bias phylogenetic
reconstruction (Lemmon et al. 2009; however, see also Wiens and Morrill
2011), therefore, we generated a second dataset utilizing a portion of the
pipeline of Breinholt et al. (2017) (alignment_DE_trim.py) to remove sites
from the alignment with <75% density, (i.e. completeness), and with
entropy >1.5 (to account for sites estimated to be nearly random).
This resulted in a trimmed alignment of 401,423 base pairs.
Lampyridae_align_clean.fasta Partition file for full alignment Partition
file for full alignment of 436 loci 2_Partition_File_for_Supp_fig_2.txt
Partition file for clean alignment Partition file for alignment file after
cleaning. 3_Partition_clean_For_Supp_fig_3.txt Lampyridae_AHE AHE
phylogeny, IQ-Tree reconstruction based on full dataset; Newick format.