DOI: 10.5061/dryad.547d7wmf6
title: Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris)

description: The saturniid moth genus Automeris includes 145 described
 species. Their geographic distribution ranges from the eastern half of
 North America to as far south as Peru. Automeris moths are cryptically
 colored and their forewings resemble dead leaves, with conspicuously
 colored, elaborate eyespots hidden on their hindwings. Despite their
 charismatic nature, the evolutionary history and relationships
 within Automeris and between closely related genera,
 remain poorly understood. In this study, we present the most comprehensive
 phylogeny of Automeris to date, including 80 of the 145 described
 species. We also incorporate two morphologically similar hemileucine
 genera, Pseudautomeris and Leucanella, as well as a
 morphologically distinct genus, Molippa. We obtained DNA data
 from both dry-pinned and ethanol-stored museum specimens and conducted
 Anchored Hybrid Enrichment (AHE) sequencing to reconstruct a high-quality
 dataset for phylogenetic analysis. The resulting phylogeny
 supports Automeris as a paraphyletic genus, with
 Leucanella and Pseudautomeris nested within, with the
 most recent common ancestor dating back to 21 mya. This study
 lays the foundation for future research on various aspects
 of Automeris biology, including anti-predator defense mechanisms,
 ecological adaptations, geographical distribution patterns, and potential
 drivers of speciation.
description: We used the “BOM1” Anchored Hybrid Enrichment probe set, which
 was developed to target 921 loci across Bombycoidea. We used this probe
 set because it has been proven effective in capturing sequence data from
 both dry-pinned and ethanol-preserved specimens. AHE sequences were
 assembled using an Iterative Baited Assembly (IBA) approach. This involves
 using the original sequencing probes to identify matching raw reads, which
 are then assembled into a novel probe. Sequences were
 aligned using MAFFT v7.245 and a 50% consensus was generated using
 FASconCAT-G v1.02  with the ‘-c -c -c’ command to result in one sequence
 per locus per specimen. To minimize the extent of missing data in the
 final concatenated dataset, loci that were only obtained from three or
 fewer species were excluded from the datasets. Loci were concatenated
 across all species into one supermatrix using FASconCAT-G with the ‘-s’
 command. Phylogenetic inference was conducted on
 concatenated supermatrices using a maximum likelihood analysis with IQTREE
 v. 1.5. Divergence time estimation was performed using
 BEAST v2.6.7 using a fixed ultrametric tree generated by IQTREE. We added
 a MultiMonophyleticConstraint prior to increase precision and
 accuracy.
description: Excel, DNA alignment software, phylogenetic tree viewer software,
 BEAST v2.6.7.
description: # Phylogeny and divergence time estimation of Io moths and relatives
 (Lepidoptera: Saturniidae: *Automeris*) --- We used the “BOM1” Anchored
 Hybrid Enrichment probe set, which was developed to target 921 loci across
 Bombycoidea. We used this probe set because it has been proven effective
 in capturing sequence data from both dry-pinned and ethanol-preserved
 specimens. AHE sequences were assembled using an Iterative Baited Assembly
 (IBA) approach. This involves using the original sequencing probes to
 identify matching raw reads, which are then assembled into a novel probe.
 Sequences were aligned using MAFFT v7.245 and a 50% consensus was
 generated using FASconCAT-G v1.02  with the ‘-c -c -c’ command to result
 in one sequence per locus per specimen. To minimize the extent of missing
 data in the final concatenated dataset, loci that were only obtained from
 three or fewer species were excluded from the datasets. Loci were
 concatenated across all species into one supermatrix using FASconCAT-G
 with the ‘-s’ command. Phylogenetic inference was conducted on
 concatenated supermatrices using a maximum likelihood analysis with IQTREE
 v. 1.5. Divergence time estimation was performed using BEAST v2.6.7 using
 a fixed ultrametric tree generated by IQTREE. We added a
 MultiMonophyleticConstraint before increase precision and accuracy. ##
 Description of the data and file structure #### BEAST\_Tree.tre This file
 is the output file of BEAST V2.6.7, a dated treefile using input file
 beauti.xml #### Automeris\_ProbeFlank\_Taxa\_Availability.csv This is the
 matrix containing 0/1 for species and loci according to their probe
 capture #### Automeris\_Probe\_Taxa\_Availability.csv This is a matrix
 containing 0/1 for species and loci according to their probe capture for
 only the probe dataset #### Automeris\_RAxML\_ProbeFlank\_partitions.txt
 This is a partition file partitioning the supermatrix
 Automeris_supermatrix_ProbeFlank.fas into the loci ####
 Automeris\_RAxML\_Probe\_partitions.txt This is a partition file
 partitioning the supermatrix Automeris_supermatrix_Probe.fas into the loci
 #### Automeris\_ProbeFlank\_RAxML.tre This is the output file using the
 supermatrix Automeris_supermatrix_ProbeFlank.fas and the partition file
 Automeris_RAxML_ProbeFlank_partitions.txt as inputs ####
 Automeris\_sequencing\_metadata.xlsx This is an excel file of the species
 sampled, sequenced, and used in the phylogeny ####
 Automeris\_supermatrix\_Probe.fas This is a concatenated supermatrix fasta
 file of the probe region #### Automeris\_supermatrix\_ProbeFlank.fas This
 is a concatenated supermatrix fasta file of the probe and flank region
 #### beauti.xml This is the input file that goes into BEAST V2.6.7 ##
 Sharing/Access information The Automeris_BEAST.tre is uploaded to Open
 Tree of Life at https://tree.opentreeoflife.org/curator/study/view/ot_2240
 Data was derived from museum specimens at the Florida Museum of Natural
 History. Data were processed according to the pipeline described in
 Phylogeny and divergence time estimation of Io moths and relatives
 (Lepidoptera: Saturniidae: *Automeris*).