Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris)
Data files
Apr 24, 2024 version files 232.49 MB
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Automeris_supermatrix_Probe.fas
17.63 MB
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Automeris_supermatrix_ProbeFlank.fas
214.73 MB
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BEAST_Tree.tre
121.99 KB
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README.md
3.15 KB
Abstract
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.
README: 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).
Methods
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.
Usage notes
Excel, DNA alignment software, phylogenetic tree viewer software, BEAST v2.6.7.