DOI: 10.5061/dryad.prr4xgxv8
title: Phylogenomics supports a single origin of terrestriality in Isopods.

description: 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.
description: Data was collated from public sources, genomic and transcriptomic
 data were assembled, then analysed with phylogenetics and
 molecular-dating.
description: # Phylogenomics supports a single origin of terrestriality in Isopods.
 [https://doi.org/10.5061/dryad.prr4xgxv8](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](https://doi.org/10.5281/zenodo.13383520) and GitHub: [https://github.com/jessthomasthorpe/Isopod_Phylogenomics_MS/](https://github.com/jessthomasthorpe/Isopod_Phylogenomics_MS/) ## Sharing/Access information Data was derived from Genbank ([http://ncbi.nlm.nih.gov](http://ncbi.nlm.nih.gov)) or EBI ([https://www.ebi.ac.uk)](https://www.ebi.ac.uk\)) And BOLD, the barcode of life project: ([https://boldsystems.org](https://boldsystems.org)) ## Code/Software Is available on GitHub: [https://github.com/jessthomasthorpe/Isopod_Phylogenomics_MS/](https://github.com/jessthomasthorpe/Isopod_Phylogenomics_MS/) And in the Scripts.zip file in Zenodo, [https://doi.org/10.5281/zenodo.13383520](https://doi.org/10.5281/zenodo.13383520)