Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

<p>Abstract</p> <p>Background</p> <p>Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.</p> <p>Presentation of the hypothesis</p> <p>We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.</p> <p>Testing the hypothesis</p> <p>We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.</p> <p>Implications of the hypothesis</p> <p>Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.</p> <p>Reviewers</p> <p>This article was reviewed by Pr. William Martin, Dr. David Williams (nominated by Pr. J Peter Gogarten) & Dr. James McInerney (nominated by Pr. John Logsdon).</p

Шероховатость поверхностей при финишной алмазно-абразивной обработке

Показано, что шероховатость полированной поверхности зависит от отношения частот собственных колебаний молекулярных фрагментов на поверхностях инструмента и обрабатываемой детали. На шероховатость обработанной поверхности наибольшее влияние оказывают число молекулярных фрагментов, из которых состоят частицы шлама, их наиболее вероятный размер, частоты собственных колебаний фрагментов обрабатываемого материала и инструмента, теплопроводность обрабатываемого материала и режимы обработки

Juvenile morphology of the large Antarctic canopy-forming brown alga, Desmarestia menziesii J. Agardh

Open Access via Springer Compact Agreement. We are grateful to the UK Natural Environment Research Council for funding to FCK (grants NE/D521522/1 and NE/J023094/1), in particular through the Collaborative Antarctic Science Scheme (Grant CASS-134, 2017) to FCK and LSP. Funding for cruise-based observations in 2019 was from US National Science Foundation award OPP-1744550 to CDA. We thank Kate Stanton, Teresa Murphy and Ben Robinson (British Antarctic Survey) for support with diving operations around Rothera in January–February 2018, and also Richard L. Moe (UC Berkeley) for locating specimens corresponding to the morphology described here in the UC collection. Special thanks are due to Charlie Bibby (Financial Times) for taking professional photographs of the unknown Desmarestia sp. in the aquarium of the Bonner Lab at Rothera (Fig. 2a). We would also like to thank Richard L. Moe (UC Berkeley) and Christian Wiencke (AWI Bremerhaven) for their very helpful reviews of this paper. Also, the MASTS pooling initiative (Marine Alliance for Science and Technology for Scotland, funded by the Scottish Funding Council and contributing institutions; grant reference HR09011) is gratefully acknowledged for supporting FCK. This research contributes to the SCAR Ant-ERA research programme.Peer reviewedPublisher PD

Molecular phylogenies support taxonomic revision of three species of Laurencia (Rhodomelaceae, Rhodophyta), with the description of a new genus

Systematics of the Laurencia complex was investigated using a taxon-rich data set including the chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene only and a character-rich data set combining the mitochondrial cytochrome oxidase 1 (COI-5P), the rbcL marker, and the nuclear large subunit of the ribosomal operon (LSU). Bayesian and ML analyses of these data sets showed that three species hitherto placed in the genus Laurencia were not closely related to Laurencia sensu stricto. Laurencia caspica was the sister group of the remaining Osmundea species, L. crustiformans joined Palisada and L. flexilis consisted of an independent lineage. In light of these results a new genus, Ohelopapa, was proposed to accommodate L. flexilis. This new genus is morphologically characterized by four pericentral cells in each vegetative axial segment, however it lacks corps en cerise in cortical cells and secondary pit connections between cortical cells which are characteristic in Laurencia. Three novel combinations are proposed to render the classification closer to a natural system: Ohelopapa flexilis, Osmundea caspica, and Palisada crustiformans

Algues

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Fucans and alginates without phenolic compounds

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Les végétaux marinsou le succès de poupées russes

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L’union fait la force

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Étude de l'évolution des algues brunes au moyen de phylogénies moléculaires

L étude des séquences d acides nucléiques, a permis de résoudre certaines relations phylogénétiques au sein des algues brunes, en particulier les premières divergences. Les séquences d ADN codant pour les ARNr 18S et 28S ainsi que celles du gène chloroplastique rbcL ont permis de construire les premières phylogénies complètes des Phaeophyceae qui ont montré que le genre Choristocarpus est le premier à diverger suivi successivement par l ordre des Dictyotales, celui des Sphacelariales et celui des Syringodermatales. Les autres lignées constituent un large clade, nommé clade A, constitué des représentants des autres ordres (Fucales, Laminariales s.l., Ectocarpales, Desmarestiales, Cutleriales, Tilopteridales, Sporochnales, Scytothamnales, Ralfsiales). Ces gènes ont permis de confirmer le caractère monophylétique de la majorité des ordres et nous ont également permis de préciser la position du genre Microzonia au sein des Syringodermatales et qui était jusqu à présent placé dans Dictyotales ou les Cutleriales. Ces résultats sont soutenus par des valeurs statistiques élevées ainsi que de nombreux caractères morphologiques. Cependant ces marqueurs moléculaires n ont pas permis de résoudre les relations entre les ordres à l intérieur du clade A. La recherche d autres marqueurs s est donc avérée nécessaire. Les gènes chloroplastiques codant le tufA et l' atpB ont été choisis et ajoutés à notre jeu de données pour résoudre les relations inter-ordinales au sein du clade A. Ces nouvelles séquences ont permis d établir de nouvelles relations phylogénétiques au sein du clade A où trois groupes monophylétiques ont été mis en évidence.The study of nucleic acid sequences, allowed us to resolve several phylogenetic relationships within brown algae, particularly the first divergences. The first comprehensive phylogenies of the Phaeophyceae were built using rDNA sequences coding for 18S and 28S rRNA and chloroplastic rbcL. Genus Choristocarpus is the first to diverge followed successively by the orders Dictyotales, Sphacelariales and Syringodermatales. The other lineages form a large clade, here called clade A. It includes the following orders : Fucales, Laminariales s.l., Ectocarpales, Desmarestiales, Cutleriales, Tilopteridales, Sporochnales, Scytothamnales and Ralfsiales. The monophyly of the majority of orders was confirmed and the genus Microzonia - until now placed within either Dictyotales or Cutleriales - was moved in Syringodermatales. These results are supported by high statistical values and numerous morphological characters. However relationships within the clade A were not resolved. In order to improve the knowledge of inter-ordinal relationships within the clade A chloroplastic genes coding tufA and atpB were chosen and added to our dataset. Three monophyletic groups were highlighted.PARIS-BIUSJ-Physique recherche (751052113) / SudocBANYULS/MER-Observ.Océanol. (660162201) / SudocPARIS-Museum-Bib. Botanique (751052309) / SudocSudocFranceF

Catalogue illustré des types conservés à PC des espèces historiquement placées dans le genre &lt;I&gt;Lessonia&lt;/I&gt; (Laminariales, Phaeophyceae), incluant une étude systématique de trois espèces sud-américaines avec une description de &lt;I&gt;L. searlesiana&lt;/I&gt; ...

Des spécimens argentins du genre Lessonia provenant de Terre de Feu et les types de ce genre conservés à PC, ainsi que des spécimens provenant des îles Kerguelen ont été examinés, en particulier au plan anatomique. Lors de la distinction entre les deux espèces L. flavicans et L. vadosa (Searles, 1978), le nom L. flavicans avait été attribué à une espèce dépourvue de lacunes corticales et vivant en eau profonde car les lacunes présentes dans le matériel type de Bory de Saint-Vincent étaient passées inaperçues. Or, des lacunes corticales existent aussi bien dans le matériel type de L. flavicans Bory de Saint-Vincent in d\u27Urville que dans celui de L. vadosa Searles. Par cette caractéristique comme par les autres, le matériel type de Bory correspond en fait à l\u27espèce actuellement nommée L. vadosa et non à l\u27espèce nommée L. flavicans. L. vadosa devient donc un synonyme taxinomique de L. flavicans et L. flavicans sensu Searles (1978) n\u27a donc plus de nom; en conséquence, l\u27espèce nouvelle L. searlesiana est proposée pour ce taxon et un spécimen holotype est désigné parmi les spécimens de Searles. En outre, le spécimen qui avait été désigné comme le lectotype de L. flavicans parmi le matériel rapporté du voyage de la Coquille ne pouvait en fait pas être éligible au statut de syntype; un nouveau lectotype a donc été désigné dans cet article. Le matériel type des espèces historiquement placées dans le genre Lessonia et conservé à PC est illustré.Specimens of Lessonia from Fuegia and types housed at PC, as well as specimens from Kerguelen Islands were examined with special reference to anatomical features. When separating L. flavicans from L. vadosa (Searles, 1978), the name L. flavicans had been assigned to a deep water species without cortical lacunae because the lacunae present in Bory de Saint-Vincent\u27s type material had been overlooked. Actually, lacunae of the cortex are present in type material of both L. flavicans Bory de Saint-Vincent in Dumont d\u27Urville and L. vadosa Searles. On this basis and considering the other morphological features as well, Bory\u27s type material corresponds actually to the species currently named L. vadosa and not to the one named L. flavicans. L. vadosa becomes thus a taxonomic synonym of L. flavicans and L. flavicans sensu Searles (1978) has no name anymore; the new species L. searlesiana is thus proposed for it and a holotype is designated among Searles\u27 original material. Furthermore, the specimen previously designated as the lectotype of L. flavicans among the material collected during the Coquille expedition was actually not eligible as possible syntype and a new lectotype is therefore designated here. Type material of taxa historically assigned to the genus Lessonia and preserved at PC is illustrated.</p