Complex patterns of local adaptation in teosinte

Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and a good understanding of population structure. We have used environmental and high-density genotype data to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found that altitude, dispersal events and admixture among subspecies formed a complex hierarchical genetic structure within teosinte. Patterns of linkage disequilibrium revealed four mega-base scale inversions that segregated among populations and had altitudinal clines. Based on patterns of differentiation and correlation with environmental variation, inversions and nongenic regions play an important role in local adaptation of teosinte. Further, we note that strongly differentiated individual populations can bias the identification of adaptive loci. The role of inversions in local adaptation has been predicted by theory and requires attention as genome-wide data become available for additional plant species. These results also suggest a potentially important role for noncoding variation, especially in large plant genomes in which the gene space represents a fraction of the entire genome

Implementation of early intensive behavioural intervention for children with autism in Switzerland

Abstract Background There is a major gap between the US and most European countries regarding the implementation of early intensive behavioural intervention (EIBI) for children with autism. The present paper reports on the current status of EIBI in Switzerland and on the effectiveness of EIBI under clinical conditions in a Swiss pilot project. Methods The paper combines a narrative report of the care system for children with autism in Switzerland and an initial evaluation of EIBI as implemented in the Department of Child and Adolescent Psychiatry, University of Zurich. Results The current situation of the implementation of EIBI for children with autism in Switzerland is characterized by marked deficits in its acceptance. Major reasons include insufficient governmental approval and lacking legal and financial support. In addition, ignorance among health care providers and educational professionals has contributed to this situation precluding that children with autism receive the most beneficial assistance. The authors have initiated and been working in an intervention centre offering EIBI for a decade and report on their experience with the implementation of EIBI. Based on their clinical practice, they document that EIBI also works efficiently under ordinary mental health service conditions. Conclusions EIBI needs to be implemented more intensively in Switzerland. Although the effects of EIBI as implemented in Zurich are promising, the results are not as pronounced as under controlled research conditions

Vegetation and disturbance history of the Bavarian Forest National Park, Germany

National parks are supposed to protect large-scale ecological processes, along with species and ecosystems. Detailed knowledge about past vegetation and disturbance regimes therefore forms an important basis for appropriate management. In the Bavarian Forest National Park in SE Germany, we therefore studied fossil pollen, spores and macrofossils from lake Rachelsee, a nearby mire, and Stangenfilz mire, all lying at higher elevations. Results indicate that deciduous forest on lower slopes (ca. 500–1,000 m a.s.l.) were first affected by humans in Neolithic times ca. 4500 bc with marked declines of Tilia, Ulmus and Fraxinus. High-montane mixed forests (1,000–1,450 m a.s.l.) were in a near-natural state consisting of Picea, Abies and Fagus in comparable proportions up to ca. 500 bc (a natural baseline condition), after which they were impacted by forest grazing and/or logging, starting between early-Roman times to early-Medieval times depending on location. Abies especially declined markedly. Forest partially recovered during the migration period fifth-eighth century ad, especially Carpinus, but not Abies. Subsequently, deforestation increased at lower elevation for food production, and forest grazing and wood extraction at higher elevation led to a further strong decline of Abies around ad 1000 near Rachelsee. After that, nutrient levels increased continually at all elevations, and a forest fire occurred in the 13th century near Stangenfilz. During the 19th century, forests around Rachelsee recovered partially whereas overgrazing of Stangenfilz resulted in a hiatus. Forests declined further in the 20th century around the study sites, but after ca. ad 1960 less so around Rachelsee thanks to local conservation measures. Historically recorded large-scale bark-beetle infestations following heavy storms, such as in the ad 1870s and 1980s, hardly left traces in the pollen data. From a palaeoecological perspective the Park’s no-intervention management strategy is well-suited to facilitate recovery of original forest functioning and diversity, as it is slowly leading to renewal of natural mixed forest of Abies, Picea and Fagus. This development may have considerable influence on the future disturbance regime, and the insights obtained will be important for the park management

How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort.

During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses

How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort

Background During the SARS-CoV-2 pandemic, many countries directed substantial resources towards genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. Aim We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic dataset from Switzerland, comprising more than 143k sequences. Methods We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. Results The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. Conclusion A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage dependent – something that is unknown at the time of sequencing – and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs