Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?

SIMPLE SUMMARY: New technological advancements often radically change our views on the world. Sequencing of DNA and use of it to reconstruct the evolution of organisms was an advancement that revolutionised human understanding of the origin of nematodes and interrelationships within this often neglected but diverse and important group of animals. This manuscript provides a summary of current knowledge and opinions on the relationships within nematodes, indicates where further research is needed and briefly discusses some of the most common problems and errors in molecular phylogeny of the phylum Nematoda. ABSTRACT: Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.