Short Course SC1.1: Data Assimilation in the Geosciences - Practical Data Assimilation with the Parallel Data Assimilation Framework

Data assimilation combines observational data with a numerical model. It is commonly used in numerical weather prediction, but is't also applied also in oceanography and hydrology. The integrating observations with models in a quantitative way, data assimilation allows to estimate and improve the model states, e.g. to initialize model forecasts. Also it can estimate parameters that control processes in the model or fluxes, which can be difficult and even impossible to measure. As such data assimilation can use observations to provide information about unobservable quantities if the model represents those. The combination of model and observation requires to have error estimates of both information sources. In ensemble data assimilation the error in the model state is estimated by an ensemble of model state realizations. This ensemble not only provides estimates of uncertainties, but also of cross-correlations between different model variables or parameters. The ensemble information is then used by the assimilation method, whose most widely known is the ensemble Kalman filter. To simplify the implementation and use of ensemble data assimilation, the Parallel Data Assimilation Framework - PDAF - has been developed. PDAF is a freely-available open-source software (http://pdaf.awi.de) that provides ensemble-based data assimilation methods like the ensemble Kalman filter, but also support to perform ensemble simulations. PDAF is designed so that it can be used from small toy problems running on notebook computers up to high-dimensional Earth Systems models running on supercomputers. This short course aims at geoscientists who have a modeling application or observations and are interested in applying data assimilation, but haven't found a starting point yet. The course will first provide an introduction to the ensemble data assimilation methodology. Then, it will explain the implementation concept of PDAF and finally provide a hands-on example of building a data assimilation system based on a numerical model. This practical introduction will prepare the participants to build a data assimiliton system by combining their numerical model with PDAF, hence providing a quick starting point for apply the ensemble data assimilation

Intercontinental Admixture and Stratification of the European Background

The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time

Mesoporous Titania powders: the role of precursors, ligand addition and calcination rate on their morphology, crystalline structure and photocatalytic activity

We evaluate the influence of the use of different titania precursors, calcination rate, and ligand addition on the morphology, texture and phase content of synthesized mesoporous titania samples, parameters which, in turn, can play a key role in titania photocatalytic performances. The powders, obtained through the evaporation-induced self-assembly method, are characterized by means of ex situ X-Ray Powder Diffraction (XRPD) measurements, N2 physisorption isotherms and transmission electron microscopy. The precursors are selected basing on two different approaches: the acid-base pair, using TiCl4 and Ti(OBu)4, and a more classic route with Ti(OiPr)4 and HCl. For both precursors, different specimens were prepared by resorting to different calcination rates and with and without the addition of acetylacetone, that creates coordinated species with lower hydrolysis rates, and with different calcination rates. Each sample was employed as photoanode and tested in the water splitting reaction by recording I-V curves and comparing the results with commercial P25 powders. The complex data framework suggests that a narrow pore size distribution, due to the use of acetylacetone, plays a major role in the photoactivity, leading to a current density value higher than that of P25

Late Pleistocene hydrological settings at world heritage Tsodilo Hills (NW Kalahari, Botswana), a site of ancient human occupation

Based on genetic studies, a Pleistocene Kalahari “palaeo-wetland”, which spanned the region of the Okavango Delta and the Makgadikgadi Basin, was recently considered the geographic origin of evolutionary modern humans. It was proposed that subsequent out-of-homeland migration was induced by climate shifts. The Tsodilo Hills, which are in relative proximity to the Okavango Delta, represent a site of ancient human occupation since at least 100 ka. Local hydrological dynamics were predominately controlled by climate variability and are archived in the sediments of Palaeolake Tsodilo. This study seeks to better understand the Late Pleistocene environments of the ancient Tsodilo people with a focus on palaeo-hydrological settings, which played a major role for their livelihoods. Our multidisciplinary approach included different remote sensing and geophysical methods, comprehensive application of differential GPS, and sedimentological analyses concentrating on the lake beds. Four palaeo-shorelines could be identified, three of which indicate highstands during which the Tamacha palaeo-river drained Palaeolake Tsodilo towards the Okavango Panhandle. Two highstands during MIS 3b and LGM are related to periods of largely increased fish consumption by humans as has been documented by archaeologists. The palaeolake was likely most extended about 100 ka ago or earlier, when it covered ca. 70 km2 and was 16 m deep. A single (neo-)tectonic fault could be detected. We assume that the Tamacha palaeo-river was a gateway for ancient humans to reach the Tsodilo Hills from these palaeo-wetlands. The people took advantage of the Tsodilo Hills as shelter from weather hazards and as a natural fortress against predators and elephants. Geologically, the Tsodilo Hills were comparatively calm. They represented a relatively safe haven where the social behaviour of early modern humans could evolve to a higher complexity, which relates to the fundamental question when and where modern human behaviour began

Genetic analysis of 7 medieval skeletons from the Aragonese Pyrenees

Aim To perform a genetic characterization of 7 skeletons from medieval age found in a burial site in the Aragonese Pyrenees. Methods Allele frequencies of autosomal short tandem repeats (STR) loci were determined by 3 different STR systems. Mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were determined by sequencing of the hypervariable segment 1 of mtDNA and typing of phylogenetic Y chromosome single nucleotide polymorphisms (YSNP) markers, respectively. Possible familial relationships were also investigated. Results Complete or partial STR profiles were obtained in 3 of the 7 samples. Mitochondrial DNA haplogroup was determined in 6 samples, with 5 of them corresponding to the haplogroup H and 1 to the haplogroup U5a. Ychromosome haplogroup was determined in 2 samples, corresponding to the haplogroup R. In one of them, the sub-branch R1b1b2 was determined. mtDNA sequences indicated that some of the individuals could be maternally related, while STR profiles indicated no direct family relationships. Conclusions Despite the antiquity of the samples and great difficulty that genetic analyses entail, the combined use of autosomal STR markers, Y-chromosome informative SNPs, and mtDNA sequences allowed us to genotype a group of skeletons from the medieval age

Effect of probe energy and competing pathways on time-resolved photoelectron spectroscopy signals: ring-opening reaction of 1,3-cyclohexadiene

The ring-opening dynamics of 1,3-cyclohexadiene (CHD) following UV excitation is studied using a model based on quantum molecular dynamics simulations with the ab-initio multiconfigurational Ehrenfest (AI-MCE) method coupled to the Dyson orbital approach for photoionisation cross sections. Time-dependent photoelectron spectra are calculated for probe photon energies in the range 2-15 eV. The calculations demonstrate the value of universal high-energy probes, capableof tracking the full photochemical dynamics of the molecule, as well as the benefit of more selective, lower-energy probes. The predicted signal, especially with the universal probes, becomes highly convoluted due to the contributions from multiple reaction paths, rendering interpretationdifficult unless complementary measurements and theoretical comparisons are available

Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans

Methanol along the path from envelope to protoplanetary disc

Interstellar methanol is considered to be a parent species of larger, more complex organic molecules. A physicochemical simulation of infalling parcels of matter is performed for a low-mass star-forming system to trace the chemical evolution from cloud to disc. An axisymmetric 2D semi-analytic model generates the time-dependent density and velocity distributions, and full continuum radiative transfer is performed to calculate the dust temperature and the UV radiation field at each position as a function of time. A comprehensive gas–grain chemical network is employed to compute the chemical abundances along infall trajectories. Two physical scenarios are studied, one in which the dominant disc growth mechanism is viscous spreading, and another in which continuous infall of matter prevails. The results show that the infall path influences the abundance of methanol entering each type of disc, ranging from complete loss of methanol to an enhancement by a factor of >1 relative to the prestellar phase. Critical chemical processes and parameters for the methanol chemistry under different physical conditions are identified. The exact abundance and distribution of methanol is important for the budget of complex organic molecules in discs, which will be incorporated into forming planetary system objects such as protoplanets and comets. These simulations show that the comet-forming zone contains less methanol than in the precollapse phase, which is dominantly of prestellar origin, but also with additional layers built up in the envelope during infall. Such intriguing links will soon be tested by upcoming data from the Rosetta mission