Phylogenomics supports a single origin of terrestriality in Isopods.
Data files
Sep 04, 2024 version files 335.96 MB
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Isopoda.aa.fsa.phy
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Isopoda.aa.fsa.trim.phy
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Isopoda.aa.mafft.phy
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Isopoda.aa.mafft.trim.phy
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Isopoda.marker-gene.phy
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Isopoda.nt.fsa.phy
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Isopoda.nt.fsa.trim.phy
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Isopoda.nt.mafft.phy
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Isopoda.nt.mafft.trim.phy
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Isopoda.ribosomal.uncut.nex
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README.md
Abstract
Terrestriality, the adaptation to life on land, is one of the key evolutionary transitions, occurring numerous times across the tree of life. Within Arthropoda, there have been several independent transitions: in hexapods, myriapods, arachnids and isopods. Isopoda is a morphologically diverse order within Crustacea, with species adapted to almost every environment on Earth. The order is divided into 11 suborders with the most speciose, Oniscidea, including terrestrial isopods such as woodlice and sea-slaters. Recent molecular phylogenetic studies have challenged traditional isopod morphological taxonomy, suggesting that several well-accepted suborders, including Oniscidea, may be non-monophyletic. This implies that terrestriality may have evolved multiple times. Current molecular hypotheses, however, are based on limited sequence data. Here, I collate available genome and transcriptome datasets for 36 isopods and four peracarid crustaceans from public sources, generate assemblies, and use 970 single-copy orthologues to estimate isopod relationships and divergences times with molecular dating. The resulting phylogenetic analyses support monophyly of terrestrial isopods and suggest conflicting relationships based on nuclear ribosomal RNA sequences may be caused by long-branch attraction. Dating analyses suggest a Carboniferous-Permian origin of isopod terrestriality, much more recently than other terrestrial arthropods.
README: Phylogenomics supports a single origin of terrestriality in Isopods.
https://doi.org/10.5061/dryad.prr4xgxv8
Alignment files for each dataset analysed.
Description of the data and file structure
Amino-acid alignment files for phylogenomic dataset aligned with mafft or fsa, with and without trimming:
Isopoda.aa.fsa.phy
Isopoda.aa.fsa.trim.phy
Isopoda.aa.mafft.phy
Isopoda.aa.mafft.trim.phy
Nucleotide alignment files for phylogenomic dataset aligned with mafft or fsa, with and without trimming:
Isopoda.nt.fsa.phy
Isopoda.nt.fsa.trim.phy
Isopoda.nt.mafft.phy
Isopoda.nt.mafft.trim.phy
Nuclear ribosomal alignments, indicating non-aligned, removed sections of genes for marker-gene dataset:
Isopoda.ribosomal.uncut.nex
Nucleotide alignment file including all genes, for marker-gene dataset:
Isopoda.marker-gene.phy
Scripts for figures:
Scripts.zip
Available on Zenodo: https://doi.org/10.5281/zenodo.13383520 and GitHub: https://github.com/jessthomasthorpe/Isopod_Phylogenomics_MS/
Sharing/Access information
Data was derived from Genbank (http://ncbi.nlm.nih.gov) or EBI (https://www.ebi.ac.uk)
And BOLD, the barcode of life project: (https://boldsystems.org)
Code/Software
Is available on GitHub: https://github.com/jessthomasthorpe/Isopod_Phylogenomics_MS/
And in the Scripts.zip file in Zenodo, https://doi.org/10.5281/zenodo.13383520
Methods
Data was collated from public sources, genomic and transcriptomic data were assembled, then analysed with phylogenetics and molecular-dating.