A transcriptomic approach to ribbon worm systematics (nemertea): resolving the pilidiophora problem

Area of Science:

• Evolutionary Biology
• Genomics
• Zoology

Background:

• Standard Sanger sequencing methods struggle to resolve deep evolutionary relationships in ancient animal lineages.
• Previous gene-targeted approaches for Nemertea (ribbon worms) resolved many clades but left key phylogenetic uncertainties.
• Resolving nemertean phylogeny is crucial for understanding broader animal evolution.

Purpose of the Study:

• To reassess the phylogeny of the phylum Nemertea using a phylogenomic approach.
• To resolve ambiguous phylogenetic patterns and settle prior debates on ribbon worm evolutionary history.
• To evaluate the utility of Illumina-based phylogenomic data matrices for resolving deep evolutionary relationships.

Main Methods:

• Utilized phylogenomic analysis with Illumina-based de novo assembled transcriptomes.
• Employed automatic orthology prediction methods to identify homologous genes.
• Analyzed a concatenated data set of 2,779 genes (411,138 amino acids) under various evolutionary models.

Main Results:

• Generated a well-supported phylogeny recovering all major accepted nemertean clades.
• Demonstrated strong support for the monophyly of Heteronemertea, Hoplonemertea, and Monostilifera.
• Resolved ambiguous patterns, including the monophyly of Palaeonemertea and Pilidiophora, which were previously uncertain.

Conclusions:

• The phylogenomic approach using Illumina transcriptomes effectively resolved deep evolutionary relationships in Nemertea.
• The results provide a robust phylogeny that settles prior debates on ribbon worm evolutionary history.
• Highlights the importance, feasibility, and completeness of phylogenomic data matrices generated with Illumina sequencing.