Data from: hiding in plain sight: phylogenomics reveals a new branch on the Noctuoidea tree of life
Data files
Nov 13, 2023 version files 2.96 GB
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Assembled_Scranciidae.zip
1.23 MB
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datasets.zip
23.57 MB
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DiscoVista.zip
1.14 MB
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individual_loci_gene_trees.zip
7.79 MB
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NSORT_statistics.pdf
252.12 KB
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raw_files.zip
2.93 GB
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README.md
2.42 KB
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topology_testing.zip
105.42 KB
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Trees.zip
1.97 MB
Abstract
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.
README: 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
Methods
Anchored hybrid enrichment phylogenomics using the LEP1 probe kit was the primary source of molecular data studied in the present work.