Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of the group. Here, we reconstruct the most comprehensive phylogeny of Brachyura to date using sequence data of six nuclear protein-coding genes and two mitochondrial rRNA genes from more than 140 species belonging to 58 families. The gene tree confirms that the "Podotremata," are paraphyletic. Within the monophyletic Eubrachyura, the reciprocal monophyly of the two subsections, Heterotremata and Thoracotremata, is supported. Monophyly of many superfamilies, however, is not recovered, indicating the prevalence of morphological convergence and the need for further taxonomic studies. Freshwater crabs were derived early in the evolution of Eubrachyura and are shown to have at least two independent origins. Bayesian relaxed molecular methods estimate that freshwater crabs separated from their closest marine sister taxa ~135 Ma, that is, after the break up of Pangaea (∼200 Ma) and that a Gondwanan origin of these freshwater representatives is untenable. Most extant families and superfamilies arose during the late Cretaceous and early Tertiary.
Information on genetic diversity of picoeukaryotes (o2-3 lm) comes mainly from traditional gene cloning and sequencing, but this method suffers from cloning biases and limited throughput. In this study, we explored the feasibility of using the cloning-independent and massively parallel 454 pyrosequencing technology to study the composition and genetic diversity of picoeukaryotes in the coastal waters of the subtropical western Pacific using the hypervariable V4 region of the 18S rRNA gene. Picoeukaryote assemblages between two sites with different hydrography and trophic status were also compared. The approach gave a high coverage of the community at genetic difference X5% but still underestimated the total diversity at a genetic difference p2%. Diversity of picoeukaryotes was higher in an oligomesotrophic bay than in a eutrophic bay. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups comprising approximately 27, 19, 11 and 11%, respectively, of the picoeukaryotes. Water samples collected from the two bays contained different high-level taxonomic groups and phylotype operational taxonomic units of picoeukaryotes. Our study represents one of the first and most comprehensive examinations of marine picoeukaryotic diversity using the 454 sequencing-by-synthesis technology.
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The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.
One of the systematically controversial superfamilies in Caridea is the predominately deep-sea or cold water Pandaloidea, largely because this species-rich group of nearly 200 species in 25 genera exhibits a very high diversity of body forms and ecology. Although the relationships amongst the taxa within Pandaloidea have been repeatedly discussed based on morphology, no comprehensive molecular phylogeny exists. In this study, we present the first molecular phylogeny of the group, based on a combined dataset of two mitochondrial (12S and 16S rRNA) and six nuclear (ATP synthase β-subunit, enolase, glyceraldehyde-3-phosphate dehydrogenase, histone 3, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase α-subunit) markers, based on 62 species (about 1/3 of known biodiversity) in 22 genera (88% of genera) of two pandaloid families (Pandalidae, Thalassocarididae) and outgroups from seven other caridean families. With generally high support, the relationships within the clade are fully resolved. Pandalidae is shown to be paraphyletic with Thalassocarididae deeply nested within as a monophyletic group, and the latter is herein considered to be a synonym of Pandalidae. Five major clades are recovered, with the shallow water genera Anachlorocurtis, Chlorocurtis, Chlorotocella and Miropandalus forming a sister clade to the remaining genera. At the genus level, the phylogeny indicates Plesionika, Heterocarpus and Pandalus to be not monophyletic. The validity of Pandalopsis, Stylopandalus and Calipandalus is challenged and these genera are considered herein to be junior synonyms of Pandalus (Pandalopsis) and Plesionika (Stylopandalus and Calipandalus). Although not fully resolved, some evidence potentially considers Nothocaris to be a valid genus. Ancestral State Reconstruction successfully recovered 15 synapomorphies for the major clades, with 11 of them reported to be of systematic significance for the first time.
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