Molecular Phylogeny of the Astrophorida (Porifera, Demospongiaep) Reveals an Unexpected High Level of Spicule Homoplasy

Background: The Astrophorida (Porifera, Demospongiae(rho)) is geographically and bathymetrically widely distributed. Systema Porifera currently includes five families in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown and hypotheses based on morphology largely untested. Astrophorida taxa have very diverse spicule sets that make them a model of choice to investigate spicule evolution. Methodology/Principal Findings: With a sampling of 153 specimens (9 families, 29 genera, 89 species) covering the deep- and shallow-waters worldwide, this work presents the first comprehensive molecular phylogeny of the Astrophorida, using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 59 end terminal part of the 28S rDNA gene (C1-D2 domains). The resulting tree suggested that i) the Astrophorida included some lithistid families and some Alectonidae species, ii) the sub-orders Euastrophorida and Streptosclerophorida were both polyphyletic, iii) the Geodiidae, the Ancorinidae and the Pachastrellidae were not monophyletic, iv) the Calthropellidae was part of the Geodiidae clade (Calthropella at least), and finally that v) many genera were polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Conclusion: The Astrophorida is a larger order than previously considered, comprising ca. 820 species. Based on these results, we propose new classifications for the Astrophorida using both the classical rank-based nomenclature (i.e., Linnaean classification) and the phylogenetic nomenclature following the PhyloCode, independent of taxonomic rank. A key to the Astrophorida families, sub-families and genera incertae sedis is also included. Incongruences between our molecular tree and the current classification can be explained by the banality of convergent evolution and secondary loss in spicule evolution. These processes have taken place many times, in all the major clades, for megascleres and microscleres

The complete mitochondrial genome of the Antarctic sea spider Ammothea carolinensis (Chelicerata; Pycnogonida)

Mitochondria are responsible for the oxidative phosphorylation process. Accordingly, putatively adaptive changes in their genomic features have been variously associated with major eco-physiological shifts in animal evolution, including increased metabolic rates and heat adaptation. Antarctic pycnogonids offer an interesting system to test whether the selective pressure for heat production and increased aerobic metabolism may be driving genomic changes like: (a) unusual compositional biases at the nucleotide and amino acid level, possibly related to cold adaptation; (b) an accelerated rate of mutations/genomic rearrangements, possibly related to the mutagenic effects of oxygen intermediates. The complete mitochondrial genome (mtDNA) of the Antarctic sea spider Ammothea carolinensis Leach, 1814 (Arthropoda: Pycnogonida), the type species for the genus Ammothea, has been determined and is here compared to known genomes from Antarctic and temperate species. We describe a marked heterogeneity in base composition skewness parameters as well as a strong signature of purifying selection toward an increase in thymines at second codon positions, possibly associated with an increased stability of hydrophobic inter-membrane domains. We further observe a fairly high rate of genomic changes, including a possible hot spot of recombination at the level of tRNA-Q. Nevertheless, these features do not seem to be restricted to the two Antarctic pycnogonids analyzed, as to suggest a causal relationship between cold adaptation and genomic changes, and are better interpreted as basal features shared by the entire group. The relevance of the newly determined sequence for the phylogeny of pycnogonids, including its base composition and genomic rearrangements, is further discussed