Molecular phylogenetic analyses of crustaceans
Final Report Abstract
The phylogeny of crustaceans is highly debated and there was never a plausible hypothesis about the relationships between major taxa. This is the consequence of a) the very old age of many lineages, which already existed in the Paleozoic, some even may be of Cambrian origin, and b) the high morphological specialization of most groups (e.g. Mystacocarida, Copepoda, Ostracoda, Cirripediaetc.). It was even not clear if Crustacea are mono-, poly- or paraphyletic. At the beginning of our project only few molecular data were available for the inference of phylogeny. Sequences were short and only few genes had been considered, wherefore it had to be assumed that sampling errors and noise in the data would produce artefacts. In the course of our project, sequencing technologies advanced significantly. We were able to sequence several transcriptomes and compiled data of 30 crustacean species. Our largest alignment encompassed 866,479 amino acid positions and 1,886 genes. The studies were conducted mainly by B. von Reumont. Adding further data for other arthropods we gained new evidence for the paraphyly of crustaceans. Especially relevant is the evidence for the close genetic similarity between Remipedia and insects: Our results demonstrate that the different ways to compile an initial data set of core orthologs and the selection of data subsets by matrix reduction can have marked effects on the reconstructed phylogenetic trees. Nonetheless, all eight data sets strongly support Pancrustacea with Remipedia as the sister group to Hexapoda. This is the first time that a sister group relationship of Remipedia and Hexapoda has been inferred using a comprehensive phylogenomic data set that is based on EST data. We also show that selecting data subsets with increased overall signal can help to identify and prevent artifacts in phylogenetic analyses. Remipedes are a small and enigmatic group of crustaceans, first described only 30 years ago. They live in anchialine caves and have a morphology similar to that of Myriapoda. Morphological characters studied in the course of the DFG-Priority Programm by J.W. Wägele also suggest that Remipedia are closely related to insects, however, with Myriapoda as sistergroup to insects, both forming the clade Tracheata. The sistergroup of Tracheata are the Remipedia. In the molecular analyses, Myriapoda slip down the tree and appear close to Chelicerata at the base of the arthropod tree. Morphological evidence therefore suggests that molecular analyses may fail under certain circumstances. A third study led by P. Kück and dedicated to the discovery of methodological errors in maximum likelihood analyses of sequence data indeed led to the discovery of systematic errors of these methods. Simulation data with known sequence structure and history of sequence evolution demonstrate that disparity of branch lengths produce artefacts that cannot be corrected with the currently used analysis tools.
