Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements?

The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions

Preliminary characterization of echinoderm assemblages in circalittoral and bathyal soft bottoms of the northern Alboran Sea

Echinoderms, with 7.272 species described so far (based on WORMS), provide an ecosystemic role which can be important depending on their habitat, and including tag species (Manjón-Cabeza et al., 2014; Palma-Sevilla 2015) or even dominant ones (Iken et al., 2010; Hughes et al., 2012). Despite the increasing knowledge on their taxonomy, studies on ecological and assemblage composition and structure of echinoderms are very scarce compared to those for other invertebrate groups, being this information essential for improving the knowledge on Mediterranean ecosystems (Coll et al., 2010). The Alboran Sea, in the junction of the Atlantic Ocean and the Mediterranean Sea and the European and African continental margins, represents a biodiversity hotspot due to the overlapping of species from those basins and continents, including some endemic components (Coll et al., 2010). Regarding echinoderms of the Alboran Sea, most previous studies focussed on infralittoral bottoms, with very few for circalittoral and bathyal ones (Manjón-Cabeza et al, 2014; Sibuet, 1974). Nevertheless, these studies generally included faunistic lists (Ocaña & Pérez-Ruzafa, 2004; Manjón-Cabeza et al., 2014), sometimes with identification keys, ecological and distributional data of some species and rarely on the assemblage composition and structure (Palma-Sevilla, 2015), which represent the main aim of this study on echinoderm assemblages of circalittoral and bathyal soft bottoms of the Alboran Sea. During the MEDITS survey expeditions (April-May 2014-2015) on board the R/V Miguel Oliver (Fig. 1), 35 samples were collected using a beam trawl (horizontal and vertical openings of 1.3 and 1.2 m, respectively, and a mesh size of 10 mm in the codend) at depths from 40 to 774 m in the Alboran Sea (Fig. 1). Hauls were done at a speed of ca. 2 knots during 5-10 (shelf stations) and 15 minutes (slope stations). Echinoderms were separated, identified to the lowest possible taxonomic leveland specimens counted and weighed to the nearest 0.5 g. Abundance and biomass data were standardized to 1000 m2 according to the sampling area of each haul. Echinoderm assemblages were characterized according to the dominance and frequency of occurrence of species in the samples and considering different ecological indexes. Multivariate methods (CLUSTER, nMDS, SIMPER, ANOSIM) were applied, based on the Bray & Curtis similarity index, for detecting and contrastingassemblages in relation to depth and 4 geographic areas of the Alboran Sea with different influence of Atlantic waters (Occidental-Esteponato Málaga, Central-Málaga to Motril, Oriental-Motril to Almería and Alboran Island). Fig. 1. Location of beam-trawl samples (dots) collected during 2014 and 2015 MEDITS expeditions in the northern Alboran Sea. At present 39 taxa have been detected, mostly belonging to Ophiuroidea and Asteroidea (28.2 and 25.6% of all species, respectively), followed by Holothuroidea (23.1%), Echinoidea (17.9%) and Crinoidea (5.1%). Regarding abundance, a total of 54689 individuals have been collected, being Ophiuroidea (98.6% of all individuals), Holothuroidea (0.6%) and Crinoidea (0.4%) the top-dominant classes. Regarding biomass, ophiuroids also dominated (52.8%), followed by asteroids (16.1%) and holothuroids (15.0%). Considering other faunistic groups, echinoderms were the most abundant phyllum in the samples (60.7%) and the fifth one in biomass (7.6%). The dominant (for both abundance and biomass) and frequent genera included Ophiocten (displaying dominances >90%) Hymenodiscus, Luidia and Astropecten for asteroids, Antedon and Leptometra for crinoids, Dendrochirotida and Molpadidae for holothuroids, and Brissopsis and Echinocyamus for echinoids (Fig. 2). Fig. 2. Some echinodermscollected in circalittoral and bathyal soft bottoms of the Alboran Sea using beam-trawl during the MEDITS expeditions. A: Ophiocten; B: Dendrochirotida sp.; C: Brissopsis; D: Anseropoda; E: Luidia. Multivariate analyses indicated groupings of samples and significantly different echinoderm assemblages in relation to depth (RANOSIM=0.22, p0.05). Shelf assemblages displayed lower intra-group similarities (<20% similarity in SIMPER) than the slope ones (ca. 40%). Species characterizing the shelf assemblages belonged to the genera Astropecten, Antedon, Ophiothrix among others, whereas those of the slope belonged to the genera Luidia (L. sarsi), Hymenodiscus, Ophiocten, Leptometra and Amphiura

The Physics of Star Cluster Formation and Evolution

© 2020 Springer-Verlag. The final publication is available at Springer via https://doi.org/10.1007/s11214-020-00689-4.Star clusters form in dense, hierarchically collapsing gas clouds. Bulk kinetic energy is transformed to turbulence with stars forming from cores fed by filaments. In the most compact regions, stellar feedback is least effective in removing the gas and stars may form very efficiently. These are also the regions where, in high-mass clusters, ejecta from some kind of high-mass stars are effectively captured during the formation phase of some of the low mass stars and effectively channeled into the latter to form multiple populations. Star formation epochs in star clusters are generally set by gas flows that determine the abundance of gas in the cluster. We argue that there is likely only one star formation epoch after which clusters remain essentially clear of gas by cluster winds. Collisional dynamics is important in this phase leading to core collapse, expansion and eventual dispersion of every cluster. We review recent developments in the field with a focus on theoretical work.Peer reviewe

Variabilidade genética e fluxo gênico em populações híbridas e silvestres de pupunha acessada com marcadores RAPD

As populações híbridas de pupunha (Bactris gasipaes Kunth) acumularam variabilidade genética provenientes de raças primitivas ao seu redor, o que deveria aumentar sua variabilidade. Para testar esta hipótese, avaliou-se a variabilidade genética de populações híbridas por meio de marcadores RAPD utilizando 176 plantas mantidas no Banco Ativo de Germoplasma do INPA, Manaus-AM, sendo quatro populações híbridas [Belém (n=26); Manaus (n=38); Iquitos, Peru (n=41); Yurimáguas, Peru (n=41)], duas populações silvestres (B. gasipaes variedade chichagui) tipos 1 (n=21) e 3 (n=7), e duas amostras de espécie afim, B. riparia, e compararam-se os parâmetros genéticos com estudos das raças primitivas. Oito iniciadores RAPD geraram 88 marcadores polimórficos e 11 monomórficos. O teste de replicabilidade apresentou uma similaridade de Dice 0,67, considerado aceitável. A heterozigosidade média das populações híbridas foi 0,34 e o polimorfismo foi 87,9%, maiores que nas silvestres (0,31; 74,7%). O dendrograma das similaridades de Dice não apresentou grupos que representassem claramente as populações híbridas. O fluxo gênico entre Iquitos e Yurimáguas (Nm=12,75) e entre Iquitos e Manaus (Nm=9,47) foi alto, enquanto o fluxo entre Belém e Manaus (Nm=7,72) foi menor que o esperado, possivelmente devido à influência da raça Solimões. O alto valor de heterozigosidade em Manaus (0,31) parece ser resultado da união de duas dispersões após a domesticação: a do oeste amazônico, com Iquitos e Yurimáguas, e a do leste amazônico, com Belém, que se juntam em Manaus. No entanto, essas populações não apresentaram acúmulo de variabilidade genética tão expressiva para diferenciá-las das raças primitivas