The best of both worlds: combining lineage specific and universal bait sets in target-enrichment hybridization reactions

PREMISE: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort.METHODS AND RESULTS: Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24–31%) and Brassicaceae (35–59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%).CONCLUSIONS: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.NaturalisPlant science

Epizooic metazoan meiobenthos associated with tubeworm and mussel aggregations from cold seeps of the northern Gulf of Mexico

The abundance and higher taxonomic composition of epizooic metazoan meiobenthic communities associated with mussel and tubeworm aggregations of hydrocarbon seeps at Green Canyon, Atwater Valley, and Alaminos Canyon in depths between 1400 and 2800 m were studied and compared to the infaunal community of non-seep sediments nearby. Epizooic meiofaunal abundances of associated meiobenthos living in tubeworm bushes and mussel beds at seeps were extremely low (usually <100 ind. 10 cm−2), similar to epizooic meiofauna at deep-sea hydrothermal vents, and the communities were composed primarily of nematodes, copepods, ostracods, and halacarids. In contrast, epizooic meiobenthic abundance is lower than previous studies have reported for infauna from seep sediments. Interestingly, non-seep sediments contained higher abundances and higher taxonomic diversity than epizooic seep communities, although in situ primary production is restricted to seeps

Exoplanetary Atmospheres—Chemistry, Formation Conditions, and Habitability

Characterizing the atmospheres of extrasolar planets is the new frontier in exoplanetary science. The last two decades of exoplanet discoveries have revealed that exoplanets are very common and extremely diverse in their orbital and bulk properties. We now enter a new era as we begin to investigate the chemical diversity of exoplanets, their atmospheric and interior processes, and their formation conditions. Recent developments in the field have led to unprecedented advancements in our understanding of atmospheric chemistry of exoplanets and the implications for their formation conditions. We review these developments in the present work. We review in detail the theory of atmospheric chemistry in all classes of exoplanets discovered to date, from highly irradiated gas giants, ice giants, and super-Earths, to directly imaged giant planets at large orbital separations. We then review the observational detections of chemical species in exoplanetary atmospheres of these various types using different methods, including transit spectroscopy, Doppler spectroscopy, and direct imaging. In addition to chemical detections, we discuss the advances in determining chemical abundances in these atmospheres and how such abundances are being used to constrain exoplanetary formation conditions and migration mechanisms. Finally, we review recent theoretical work on the atmospheres of habitable exoplanets, followed by a discussion of future outlook of the field.M. Agúndez acknowledges funding support from Spanish MINECO through grants CSD2009-00038, AYA2009-07304, and AYA2012-32032 and from the European Research Council (ERC Grant 610256: NANOCOSMOS). J. Moses thanks the NASA Exoplanet Research program NNX15AN82G for support. Y. Hu is supported by the National Natural Science Foundation of China 435 (NSFC) under grants 41375072 and 41530423