Taxonomy based on morphology can be difficult. The challenges arise from different sources such as poor original descriptions, new records based on inadequate knowledge, uncritical application of general assumptions or presence of complexes of cryptic species. One example of problematic taxonomy is the genus Diopatra Audouin & Milne Edwards, 1833 (Onuphidae, Annelida) and within it the two species Diopatra aciculata and D. neapolitana. The species exhibit great similarity between them casting doubts on their validity as separate species. Our study aims to investigate whether D. aciculata and D. neapolitana should be synonymized, using an integrative taxonomic approach. Therefore, we assessed 22 morphological characters of 70 specimens including one specimen, which might have been erroneously assigned to D. dentata. Additionally, sequence information of five different molecular markers (i.e., 16S rDNA, COI, 28S, ITS1 and ITS2) was gathered to delineate possible species boundaries between these two species. Our results show some evidence for delineating the two species, but they are not conclusive due to both presence of shared morphological characters and conflicting evidence in the molecular data. Accordingly, our results neither confirm nor disprove complete speciation and both species seem to be in the grey zone of speciation. In conclusion, considering taxonomic stability and slight support by morphological characters, we still regard each as two independent species.

The annelid family Eunicidae comprises ten genera including the genus Marphysa Quatrefages, 1866. This genus is characterized by a global distribution and has considerable value in the bait industry worldwide. Therefore, the correct delimitation of species is important not only for consideration of its evolution, but also for culturing species from this genus. Marphysa sanguinea (Montagu, 1813) represents a complex of species and its global distribution is not clearly defined. Herein we describe a new species, Marphysa aegypti sp.n., belonging to the M. sanguinea group from the coastal waters of Egypt. This species, which has previously been reported as M. sanguinea, has a high commercial value as it is collected and vastly used by fishermen in Egypt. In our study, we used both molecular (COI barcoding region) and morphological species identification. Our results confirm that this polychaete, which is a common inhabitant of Egyptian coastal waters (i.e., Mediterranean Sea, Red Sea and the Suez Canal), is a distinct species. Our findings further support the view that the polychaete fauna of Egypt needs taxonomic revision. Determination of the polychaete species of Egypt, similarly to other regions of the world, is based on identification keys developed for Northern European species and lacks thorough morphological comparisons. Therefore, all previous records of M. sanguinea in coastal waters of Egypt should be reconsidered as being indeed M. aegypti sp.n.

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments.