Natural recovery of genetic diversity by gene flow in reforested areas of the endemic Canary Island pine, Pinus canariensis

The endemic pine, Pinus canariensis, forms one of the main forest ecosystems in the Canary Islands. In this archipelago, pine forest is a mosaic of natural stands (remnants of past forest overexploitation) and artificial stands planted from the 1940's. The genetic makeup of the artificially regenerated forest is of some concern. The use of reproductive material with uncontrolled origin or from a reduced number of parental trees may produce stands ill adapted to local conditions or unable to adapt in response to environmental change. The genetic diversity within a transect of reforested stands connecting two natural forest fragments has been studied with nuclear and chloroplast microsatellites. Little genetic differentiation and similar levels of genetic diversity to the surrounding natural stands were found for nuclear markers. However, chloroplast microsatellites presented lower haplotype diversity in reforested stands, and this may be a consequence of the lower effective population size of the chloroplast genome, meaning chloroplast markers have a higher sensitivity to bottlenecks. Understory natural regeneration within the reforestation was also analysed to study gene flow from natural forest into artificial stands. Estimates of immigration rate into artificially regenerated forest were high (0.68-0.75), producing a significant increase of genetic diversity (both in chloroplast and nuclear microsatellites), which indicates the capacity for genetic recovery for P. canariensis reforestations surrounded by larger natural stands

Smooth and compactly supported viscous sub-cell shock capturing for Discontinuous Galerkin methods

In this work, a novel artificial viscosity method is proposed using smooth and compactly supported viscosities. These are derived by revisiting the widely used piecewise constant artificial viscosity method of Persson and Peraire as well as the piecewise linear refinement of Klöckner et al. with respect to the fundamental design criteria of conservation and entropy stability. Further investigating the method of modal filtering in the process, it is demonstrated that this strategy has inherent shortcomings, which are related to problems of Legendre viscosities to handle shocks near element boundaries. This problem is overcome by introducing certain functions from the fields of robust reprojection and mollififers as viscosity distributions. To the best of our knowledge, this is proposed for the first time in this work. The resulting $C_0^\infty$ artificial viscosity method is demonstrated to provide sharper profiles, steeper gradients and a higher resolution of small-scale features while still maintaining stability of the method

Characterisation of Schiff base and chromophore in green proteorhodopsin by solid-state NMR

The proteorhodopsin family consists of hundreds of homologous retinal containing membrane proteins found in bacteria in the photic zone of the oceans. They are colour tuned to their environment and act as light-driven proton pumps with a potential energetic and regulatory function. Precise structural details are still unknown. Here, the green proteorhodopsin variant has been selected for a chemical shift analysis of retinal and Schiff base by solid-state NMR. Our data show that the chromophore exists in mainly all-trans configuration in the proteorhodopsin ground state. The optical absorption maximum together with retinal and Schiff base chemical shifts indicate a strong interaction network between chromophore and opsin. © Springer Science+Business Media B.V. 2007

Toward Guidelines for Harvest Intensities and Regeneration Targets with Minimal Impact Upon Retained Genetic Diversity in Central Hardwood Tree Species

There is an urgent need for a coordinated and systematic approach to the in situ conservation of the genetic resources of commercially important forest tree species in the Central Hardwoods. Effective in situ management of genetic resources would benefit from clear guidelines for how many adult trees can be harvested with minimal impact on allelic diversity. We are constructing a computer model for this purpose, and present preliminary results based upon replicate harvests of a virtual forest stand consisting of 200 adult trees. Our model explores how much regeneration is needed so that there is no more than a 10 percent risk of retaining less than 90 percent of the original allelic diversity. In the absence of regeneration, up to 55 percent of the adult trees can be harvested without exceeding the 10 percent risk level. At higher harvest intensities, locally-derived regeneration is needed to replace the alleles removed from the adult population. When all 200 adult trees are harvested, the 10 percent risk level is not exceeded if there are at least 116 regenerants, provided that these are derived from pre-harvest random mating among the adults. In the presence of substantial pollen flow from a genetically differentiated outside pollen source (e.g., 10-20 percent pollen flow), the minimum amount of regeneration needed is reduced. This indicates that outside pollen can be more efficient, relative to pollen from within the stand, at replacing alleles lost from the adult population

Bedeutung von CI-Nutzungsverhalten und CI-Anpassung für sprachproduktive Leistungen sehr früh cochleaimplantierter Kinder

Hintergrund Das Alter bei Versorgung mit einem Cochleaimplantat (CI) nimmt bei Kindern wesentlich Einfluss auf deren Lautsprachentwicklung. Als weitere potenzielle Einflussfaktoren sollten das CI-Nutzungsverhalten und die Häufigkeit der CI-Anpassungen evaluiert sowie die frühkindlichen sprachproduktiven Leistungen sehr früh CI-versorgter Kinder dargestellt werden. Methodik Die retrospektive Studie untersuchte 34 bilateral cochleaimplantierte Kinder mit einem CI-Versorgungsalter von M = 8,8 (SD = 1,7) Monaten. Im dritten Lebensjahr wurden die sprachproduktiven Leistungen, die Häufigkeit der CI-Anpassungen und das CI-Nutzungsverhalten anhand des systemintegrierten Dataloggings ausgewertet und in Bezug gesetzt. Ergebnisse Etwa die Hälfte der Kinder erzielte lebensaltersgemäße sprachproduktive Leistungen. Die CI-Nutzungsdauer lag bei rund 8 h täglich. Zeitlich am längsten befanden sich die Kinder in ruhiger Umgebung, am kürzesten in Situationen mit Sprache im Störschall. Die tägliche CI-Nutzungsdauer erwies sich als signifikanter Prädiktor für die sprachproduktiven Leistungen; die Sprachexposition erwies sich als wesentlicher Prädiktor speziell für die Wortproduktion. Die Anzahl der täglichen Kontaktabbrüche der CI-Sendespule zum Implantat sowie die Anzahl der CI-Anpassungen pro Monat waren nicht mit den sprachproduktiven Leistungen korreliert. Schlussfolgerung Sehr früh bilateral cochleaimplantierte Kinder können bereits im dritten Lebensjahr einen altersgemäßen Stand in der Sprachproduktion erreichen. Im Vergleich mit anderen Studien ist die tägliche CI-Nutzungsdauer als altersadäquat zu beurteilen. CI-Nutzungsdauer sowie die Dauer der täglichen Sprachexposition scheinen bedeutsamen Einfluss auf frühe Sprachkompetenzen zu nehmen. Diese Erkenntnisse sollten insbesondere in die prä- und postoperative Elternberatung einfließen

Different histories but similar genetic diversity and structure for black walnut in Indiana and Missouri

—Missouri and Indiana have markedly different histories of glaciation and recolonization by forest trees. These states also differ in land use patterns and degree of anthropogenic landscape change such as forest fragmentation. To determine the overall effects of these and other demographic differences on the levels of genetic diversity and structure in black walnut (Juglans nigra L.) more than 550 total black walnut trees from nine populations in Indiana and 10 in Missouri were sampled and analyzed using 12 nuclear microsatellite loci. Although genetic diversity parameters such as allelic richness and expected heterozygosity were high overall, they varied little among populations and their mean values for the two states were not significantly different. Pairwise genetic distance values between all population pairs ranged from 0.012-0.159, but no significant pattern of isolation by distance was detected. The estimate of the degree of genetic differentiation between states (FPT = 0.0009) was very small and not significant, indicating that differences between states explained an inconsequential portion of the total variance. The observed low levels of local and regional genetic structure indicate that high levels of pollen flow have buffered black walnut from the genetic consequences of founder effects and genetic drift in both geologic and recent time scales

Panzea: an update on new content and features

Panzea (http://www.panzea.org), the public web site of the project ‘Molecular and Functional Diversity in the Maize Genome’, has expanded over the past two years in data content, display tools and informational sections. The most significant data content expansions occurred for the single nucleotide polymorphism (SNP), sequencing, isozyme and phenotypic data types. We have enhanced our existing web display tools and have launched a number of new tools for data display and analysis. For example, we have implemented one that allows users to find polymorphisms between two accessions, a geographic map tool to visualize the geographic distribution of SNPs, simple sequence repeats (SSRs) and isozyme alleles and a graphical view of the placement of Panzea markers and genes/loci on genetic and physical maps. One goal of the informatics component of our project has been to generate code that can be used by other groups. We have enhanced our existing code base and have made our new tools available. Finally, we have also made available new informational sections as part of our educational and outreach efforts

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent