DOI: 10.5061/dryad.7sqv9s4x0
title: Data from: hiding in plain sight: phylogenomics reveals a new branch on the Noctuoidea tree of life

description: We analyze anchored hybrid enrichment data (AHE) from densely sampled
 tribes and subfamilies of Notodontidae (Prominent Moths). Notodontidae are
 monophyletic except for an assemblage of genera related to Thacona Walker
 (=Scrancia Holland), which had been recognized at either the tribal or
 subfamilial rank within Notodontidae. We elevate and re-describe
 Scranciidae, stat. nov. as a family distinct from the six currently
 recognized noctuoid families (Noctuidae, Erebidae, Euteliidae, Nolidae,
 Notodontidae, and Oenosandridae). Scranciidae include 22 genera comprising
 approximately 100 species—distributed in Africa, Asia, and Australia. We
 re-interpret morphological synapomorphies previously proposed for
 Notodontidae (including Scranciidae) and for the trifid Noctuoidea more
 broadly. Deep-level relationships within Noctuoidea are not well resolved
 outside the clade comprising the four quadrifid families (Noctuidae,
 Erebidae, Euteliidae, and Nolidae). The phylogenetic position of
 Scranciidae relative to Notodontidae, Oenosandridae, and the quadrifids
 varied markedly depending on data type (amino acid vs. nucleotide) and
 analytical framework (maximum likelihood, multi-species coalescent, and
 parsimony). We discuss the possible roles of missing data and short branch
 lengths in resolving the placement of Scranciidae. In the topology best
 supported by the most available data, Scranciidae are sister to the
 remaining Noctuoidea, highlighting their phylogenetic significance. We
 provide a provisional list of the genera included in Scranciidae.
description: Anchored hybrid enrichment phylogenomics using the LEP1 probe kit
 was the primary source of molecular data studied in the present
 work.
description: # Hiding in Plain Sight: Phylogenomics Reveals a New Branch on the
 Noctuoidea Tree of Life Phylogenomic study of Noctuoidea highlighting a
 new family: Scranciidae ## Description of the data and file structure
 Directory "datasets" containing all alignments for the 11
 different datasets and the corresponding partitioning schemes/models
 selected by Model Finder Directory "DiscoVista" containing
 outputs of various DiscoVista analyses except those already included as
 supplements, specifically these outputs are: * AA.block-shades.pdf which
 is a discordance analysis of species trees, rows correspond to clades and
 columns correspond to analysis, colors refer to bootstrap support for
 those clades for those analyses * AA.block.pdf is similar to the above
 AA.block-shades.pdf but instead shows whether a clade is supported or
 rejected based on branch support values, depending on the analysis,
 compatible/weakly rejected clades are not recovered in the tree(s), but
 are compatible if low supported branches are "contracted" *
 annotations.txt is an input file that assigns each taxon to one of the
 respective clades being analyzed the subdirectory GC_content includes two
 files "pTpP_GC_boxplot.pdf" and "pTpP_GC_point.pdf"
 which are boxplots and point graphs, respectively, for the GC content
 ratios for each taxon for all codon positions (all), first codon position
 (C1), second codon position (C2), and third codon position (C3) Directory
 "individual_loci_gene_trees" containing gene trees and
 individual locus alignments used to generate them Directory
 "topology_testing" IQTREE topology test outputs for AA and
 Nucleotide datasets and a directory called "constrained" trees
 that contains the constraint trees and the constrained analyses output
 from IQTREE Directory "Trees" which contains all dated and
 undated tree files output from IQ-TREE, TreePL, ASTRAL, MPBOOT, and TNT
 Directory "raw_files" are the raw fastq reads of the Scranciidae
 species newly sequenced for this study Directory
 "Assembled_Scranciidae" contains the assembled AHE LEP1 loci for
 the 5 Scranciidae sequenced for this study; each taxon subdirectory in
 /Assembled_Scranciidae contains the probe sequences, "full
 length" sequences with flanks (not used in the present study), and a
 set of assembly statistics, see Breinholt et al. (2018) for more
 information File "NSORT_statistics.pdf" includes the sorting
 results from genesortR