There is no consensus on the interrelationships of lower actinopterygians including basal teleosts and this fact influences the entire actinopterygian knowledge. This is due to several factors:
- Early syntheses are based on vague or weak theoretical backgrounds whereas newer analyses are based on an explicit phylogenetic approach.
- Phylogenetic methodology differs from trees constructed in a traditional fashion to those produced with computer algorithms (PAUP, HENNIG 86).
- Phylogenetic analyses include different taxa, between five and 50 taxa, and in most studies, Paleozoic forms and Triassic neopterygians were under-represented.
- Some hypotheses included a limited and variable number of living taxa or the opposite. Frequently, only Polypterus is included.
- Data matrices contain variable numbers of non-comparable characters.
- The recognition of homologous structures among different actinopterygians investigated by various authors, and the homology of characters between outgroups and the actinopterygian ingroup are problematic.
- Different outgroups have been used to polarize characters and root trees.
- In addition, molecular studies show that analyses of nuclear genes result in hypotheses more congruent with morphology than mitochondrial genes or entire mitochondrial genomes.
