Perspectives on Open Science and scientific data sharing::an interdisciplinary workshop

Looking at Open Science and Open Data from a broad perspective. This is the idea behind "Scientific data sharing: an interdisciplinary workshop", an initiative designed to foster dialogue between scholars from different scientific domains which was organized by the Istituto Italiano di Antropologia in Anagni, Italy, 2-4 September 2013.We here report summaries of the presentations and discussions at the meeting. They deal with four sets of issues: (i) setting a common framework, a general discussion of open data principles, values and opportunities; (ii) insights into scientific practices, a view of the way in which the open data movement is developing in a variety of scientific domains (biology, psychology, epidemiology and archaeology); (iii) a case study of human genomics, which was a trail-blazer in data sharing, and which encapsulates the tension that can occur between large-scale data sharing and one of the boundaries of openness, the protection of individual data; (iv) open science and the public, based on a round table discussion about the public communication of science and the societal implications of open science. There were three proposals for the planning of further interdisciplinary initiatives on open science. Firstly, there is a need to integrate top-down initiatives by governments, institutions and journals with bottom-up approaches from the scientific community. Secondly, more should be done to popularize the societal benefits of open science, not only in providing the evidence needed by citizens to draw their own conclusions on scientific issues that are of concern to them, but also explaining the direct benefits of data sharing in areas such as the control of infectious disease. Finally, introducing arguments from social sciences and humanities in the educational dissemination of open data may help students become more profoundly engaged with Open Science and look at science from a broader perspective

Phylogenie und Merkmalsevolution in der Gattung Crepis L. (Cichorieae, Compositae)

Artbildungsprozesse bei Pflanzen können auf Karyotypveränderungen zurückgehen. Die Dissertation von N. Enke “Phylogeny and Character Evolution in the Genus Crepis L. (Cichorieae, Compositae)” analysiert den Einfluß von chromosomalen Veränderungen auf die Artneubildung in diploiden Pflanzengruppen. Die Gattung Crepis wird modellhaft in diesem Rahmen untersucht. Crepis L. ist in der gesamten Holarktis und Afrika verbreitet mit der höchsten Diversität im Mediterranraum. Die meisten Arten der Gattung sind diploid, bis auf 15 Arten der Sektion Psilochaenia und ca. 5 andere Arten. Die Chromosomengrundzahl variiert zwischen x=3 und x=6 (7), bzw. x=11 in der Sektion Psilochaenia. Die letzte Revision der Gattung geht auf Babcock (1947, The Genus Crepis Iⅈ, University of California Press) zurück. Er gliederte 196 der über 200 heute bekannten Arten auf Grund hauptsächlich karyologischer Ähnlichkeiten, wie z.B. Chromsomenform und – zahl, in 27 Sektionen. Babcock postulierte, daß die Hauptursache von Artbildungsereignissen Änderungen des Karyotyps seien, und Hybridisierung nur eine kleine Rolle spiele. Aufbauend auf Babcocks Monografie postuliert die vorliegende Arbeit (1) phylogenetische Hypothesen für Crepis, überprüft (2) bereits bestehende Hypothesen zu Karyotypevolution und Artbildungsmechanismen in der Gattung, identifiziert (3) morphologische und anatomische Merkmale zur Definition infragenerischer Gruppen, und bewertet (4) die bestehende Gliederung in Sektionen neu. Die phylogenetischen Zusammenhänge der Gattung Crepis wurden mit Hilfe des Kernmarkers ITS und des Chloroplastengens matK rekonstruiert. Genomgrößen wurden mittels Flow Cytometry gemessen und in einem phylogenetischen Zusammenhang interpretiert. Frucht- und Pollenmerkmale, sowie die Papillae der Narbenäste wurden mittels LM und REM auf eine Eignung zur Abgrenzung infragenerischer Gruppen untersucht. Die Phylogenierekonstruktionen (ITS/matK: 123/73 Sequenzen von 78/52 Arten), unterscheiden sich in der Anordnung der apikalen Gruppen, aber unterstützen beide drei Hauptkladen: Die erste besteht aus ca. 80% der untersuchten Arten als Crepis s.str., die zweite umfasst neben den Gattungen Lapsana und Rhagadiolus alle untersuchten Arten aus fünf Crepis Sektionen, die dritte entspricht der früheren Crepis Sektion Ixeridopsis, mittlerweile Gattung Askellia. Die gemeinsame Interpretation karyologischer und molekularer Ergebnisse ließ ein komplexes Muster der Karyotypevolution erkennen. Die Chromosomengrundzahl variiert stark sowohl innerhalb als auch zwischen den Kladen. Sowohl eine Ab- als auch eine Zunahme der Chromosomengrundzahl während der Aufspaltung rezenter Arten konnte beobachtet werden, sowie eine Abnahme der Genomgröße. Annuelle haben tendenziell kleine Genomgrößen, während ausdauernde Arten eine höhere Variation zeigen. Des Weiteren besitzen Arten der Mediterranregion im Allgemeinen kleinere Genome als Arten aus N- und Mitteleuropa, Eurasien sowie Zentral- und O-Asien. Von den untersuchten Mikromerkmalen unterschied die Struktur der Pappusborsten zwischen den drei Kladen. Frucht-, Pollen- und Narbenastmerkmale zeigten auf Grund der geringen Stichprobenmenge keine interpretierbaren Muster. Die behandelten Merkmale könnten jedoch bei Einbeziehung weiterer Arten eine Eignung als Unterscheidungsmerkmal infragenerischer Gruppen aufweisen. Taxonomische Konsequenzen aus den vorliegenden Ergebnissen sind die Aufrechterhaltung der Gattungen Lapsana und Rhagadiolus, die Behandlung von Crepis als paraphyletisches Taxon und die Eingliederung der ehemaligen Gattung Dianthoseris. Anmerkungen zu einer revidierten sektionalen Gliederung der Gattung werden gemacht.Karyotype alterations play an active role in plant speciation processes. N. Enke’s dissertation “Phylogeny and Character Evolution in the genus Crepis L. (Cichorieae, Compositae)” contributes towards the understanding of the influence of karyotype changes on diversification in diploid plant genera using Crepis as model group. The genus Crepis is distributed in the Holarctic and Africa with the highest diversity in the Mediterranean. Most of the species within the genus are diploid; except for the 15 species of section Psilochaenia and approximately five additional species. The basic chromosome number in the genus ranges from x = 3 to 6 (7), respectively x = 11 in section Psilochaenia. The genus Crepis was revised by Babcock in 1947 (The genus Crepis Iⅈ, University of California Press). He assigned 196 of the over 200 species known today to 27 sections mainly due to karyological characters, such as chromosome number and shape. Babcock also postulated hypotheses on evolution and speciation within Crepis: karyotype rearrangements are the driving force of speciation, while hybridisation only plays a minor role in species formation. Based on Babcock’s monograph the present study (1) postulates phylogenetic hypotheses for Crepis, (2) reassesses existing hypotheses on karyotype evolution and speciation mechanisms within the genus, (3) identifies morphological and anatomical characters reflecting infrageneric groups, and (4) revaluates the current infrageneric classification. The phylogenetic relations within the genus are inferred from both nuclear (ITS) and chloroplast (matK) markers. Genome size is measured by flow cytometry and evaluated on a molecular phylogenetic background. Achene anatomy and morphology, pollen morphology and structure of style branch papillae are investigated via SEM and LM for their applicability to delimitate infrageneric groups. The phylogenetic reconstructions based on 123 ITS sequences of 78 species and 73 matK sequences of 52 species differ in apical branching pattern but support three main clades: the first comprises approximately 80% of sampled species as Crepis s.str., the second includes the genera Lapsana and Rhagadiolus and all sampled taxa of five Crepis sections, the third corresponds to former Crepis section Ixeridopsis; now genus Askellia. Combined karyological and molecular analyses show a complex pattern of karyotype evolution within the genus. Chromosome number is highly variable in and between clades, and de- and also increased during evolution. A trend toward a decrease in genome size within Crepis is observed. Annuals predominantly feature small genomes while in perennials genome size is variable. Species from the Mediterranean in general feature smaller genomes than species from N-Europe, Eurasia and Central/E-Asia. Of the tested microcharacters pappus structure differs between the three clades inferred by molecular analyses. Achene anatomy, pollen morphology and style branch papillae provide no evidence for infrageneric classification, mostly due to low sample size. Achene anatomy and style branch papillae show sufficient variation for systematic use if sample size is broadened. As taxonomic consequences of the presented study the genera Lapsana and Rhagadiolus are preserved and the genus Crepis is treated as paraphyletic. The former genus Dianthoseris is included into Crepis. Comments on a revised sectional classification are given

Data from: Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river system Odra and Lusatian Neisse from the source to the mouth is analysed with DNA and morphological methods, which are compared. The NGS technology almost always leads to a higher number of identified taxa (270 via NGS vs. 103 by light microscopy LM), whose presence could subsequently be verified by LM. The sequence-based approach allows for a much more graduated insight into the taxonomic diversity of the environmental samples. Taxa retrieval varies considerably throughout the river system, depending on species occurrences and the taxonomic depth of the reference databases. Mostly rare taxa from oligotrophic parts of the river systems are less well represented in the reference database used. A workflow for DNA-based NGS diatom identification is presented. 28 000 diatom sequences were evaluated. Our findings provide evidence that metabarcoding of diatoms via NGS sequencing of the V4 region (18S) has a great potential for water quality assessments and could complement and maybe even improve the identification via light microscopy

RL6.1AmphoraTree

This .mts file was generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA 6

Growth and photosynthesis characteristics of three benthic diatoms from the brackish southern Baltic Sea in relation to varying environmental conditions

Three benthic diatom taxa Navicula perminuta, Melosira moniliformis and Nanofrustulum shiloi were isolated from sublittoral sandy sediments from the brackish southern Baltic Sea and established as unialgal cultures. Growth rates were determined under controlled conditions at different incubation temperatures (7–27°C), irradiances (10–600 μmol photons m−2 s−1) and salinities (1–50). The diatoms exhibited a wide range of growth tolerance. All of them grew well with growth rates of 0.3–1.5 divisons (μ) d−1 under the given gradients of parameters, indicating a classification as euryhaline and eurythermal species. In accordance with these results, photosynthesis was characterised at optimal with suboptimal growth conditions of temperature and irradiance, using the methodological approach of oxygen production. Maximum oxygen production rates after preincubation under 150 μmol photons m−2 s−1 reached values of 120 to 360 μmol O2 mg chlorophyll a h−1. All three benthic diatoms from the Baltic Sea are physiologically well adapted to the fluctuating environmental conditions in shallow-water habitats without production loss under suboptimal conditions

Does the Cosmopolitan Diatom <i>Gomphonema parvulum</i> (Kützing) Kützing Have a Biogeography?

<div><p>Diatom cultures of the <i>G. parvulum</i> species complex were established from seven different sites in the Faroe Islands, Sweden, Germany, Mexico and Korea, and were studied in detail. Eight morphodemes were identified which corresponded to the descriptions of the cosmopolitan taxon <i>G. parvulum</i> (Kützing) Kützing sensu lato: its nominate variety (var. <i>parvulum</i>), <i>G. parvulum</i> var. <i>exilissimum</i> Grunow and <i>G. parvulum</i> f. <i>saprophilum</i> Lange-Bertalot & Reichardt, <i>G. [parvulum</i> var.] <i>lagenula</i> Kützing plus four unidentifiable morphodemes. The concatenated analysis of the sequences of the markers 18SV4, <i>rbc</i>L, and ITS as well as morphological data resulted in a separation of four taxa based on their biogeography in Mexico, Korea, central Continental Europe and Northern Atlantic Europe. Mantel tests showed a significant correlation between molecular and geographical distances. The diagnoses of two taxa, <i>G. parvulum sensu stricto</i>, and <i>G. lagenula</i>, were emended, G. <i>saprophilum</i> elevated to species rank and epitypes designated. One species was newly described.</p></div

LM photos of strains.

<p>Figs. 2.1–22. <i>Gomphonema parvulum</i> (Kützing) Kützing var. <i>parvulum</i>. Figs. 2.1–3. Strain D16_042, Figs. 2.4–6. Strain D16_044, Fig. 2.7. Strain D16_005, Fig. 2.8. Strain D16_009, Figs. 2.9–11. Strain D16_008, Figs. 2.12–15. Strain D16_004, Figs. 2.16–18. EPITYPE Strain D16_045. Figs. 2.19–20. Strain D13_034, Fig. 2.21. Strain D16_030, Fig. 2.22. Strain D16_027. Figs. 2.23. Strain D16_026, <i>Gomphonema parvulum</i> var. nov.? Figs. 2.24–25. Strain D12_022, <i>Gomphonema parvulum</i> var. <i>parvulum</i> [morphodeme exilissimum]. Figs. 2.26–28. <i>Gomphonema lagenula</i> Kützing. Figs. 2.26–27. Strain D33_006. Fig. 2.28. EPITYPE Strain D33_024. Figs. 2.29–34. <i>Gomphonema parvulum</i> var. nov.? Figs. 2.29. Strain D16_028. Figs. 2.30–34. Strain D16_011. Figs. 2.35–43. <i>Gomphonema saprophilum</i> (Lange-Bertalot & Reichardt) Abarca et al. comb. nov. Figs. 2.35–38. EPITYPE Strain D36_003. Figs. 2.39–41. Strain D20_027, Figs. 2.42–43. Strain D03_167. Figs. 2.44–49. <i>Gomphonema narodoense</i> R. Jahn et al. sp. nov. Figs. 2.44–46. HOLOTYPE Strain D23_012. Figs. 2.46–49. Strain D23_009. Scale bars represent 10 µm.</p