2026-10-14T06:31:06Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33931330 2026-09-22T08:50:03Z category_24271 item_type_3 month_year_09_2026

Rouphozoa in deep spiralian phylogenomics Oscar Wallnoefer (22667549) Giovanni Galassi (25071740) Alice Cascella (25071790) Diego Carli (25071792) M. Antonio Todaro (175761) Federico Plazzi (10683213) Phylogeny and comparative analysis Spiralia Phylogenomics Rouphozoa Gastrotricha Platyhelminthes Invertebrates <p dir="ltr"><b>Abstract</b><br>Deep phylogenetic relationships within Spiralia remain unstable despite the increasing availability of phylogenomic datasets. To investigate the sources of this instability, we assembled one of the most taxonomically comprehensive spiralian datasets currently available, comprising 75 species from 15 phyla. Moreover, we specifically addressed the clade Rouphozoa incorporating the largest phylogenomic sampling of Gastrotricha to date.<br>We explored the effects of matrix completeness, alignment trimming, compositional filtering, long-branch filtering, amino acid recoding, evolutionary models, and locus subsampling across 126 phylogenetic analyses. Alignment trimming had little influence on topology, whereas the model remains the most influential choice for the recovery of higher-level relationships. Rouphozoa emerged as one of the most stable higher-level relationships, whereas Gastrotricha monophyly remained sensitive to analytical conditions, particularly taxon representation and locus composition. Using a multivariate assessment of locus properties, we identified a subset of genes that recovered both Rouphozoa and Gastrotricha while preserving support for other major spiralian clades. 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> 2026-09-22T08:50:03Z Dataset Dataset 10.6084/m9.figshare.33931330.v1 https://figshare.com/articles/dataset/Rouphozoa_in_deep_spiralian_phylogenomics/33931330 CC BY 4.0 Open Access after 2026-10-22