Rouphozoa in deep spiralian phylogenomics

While these results strongly suggest the sister relationship between Gastrotricha and Platyhelminthes, we also suggest that instability in deep spiralian phylogeny reflects heterogeneous phylogenetic signals among loci rather than simple data deficiency. More generally, they indicate that locus quality and taxon sampling may be more important than matrix size for resolving ancient animal radiations.<br><br><b>Dataset:</b> 93 species spanning 22 phyla (outgroup included)</p><p dir="ltr"><b>├── MS80/</b> # BUSCO genes shared by >80% of species<br><b>│ ├── 01_MS80_alignments/</b> # raw matrices + MAFFT alignments</p><p dir="ltr"><b>│ ├── 02_MS80_matrices/</b> # 21 matrix types + partition files<br><b>│ ├── 03_MS80_trees/</b> # IQ-TREE3 output (partition models, PMSF)</p><p dir="ltr"><b>│ └── 04_recoding/</b> # Dayhoff-6 recoded alignments + trees<br><b>└── MS90/</b> # BUSCO genes shared by >90% of species</p><p dir="ltr"><b> ├── 01_MS90_alignments/</b> # raw matrices + MAFFT alignments<br><b> ├── 02_MS90_matrices/</b> # 21 matrix types + partition files</p><p dir="ltr"><b> ├── 03_MS90_trees/</b> # IQ-TREE3 output (partition models, PMSF)<br><b> └── 04_recoding/</b> # Dayhoff-6 recoded alignments + trees</p>