Sabine Brodbeck

Qua o là sta amo ün tal eroe plain fideltà sün seis post, cun büst sfrattamà, e stenda il bratsch our da spelm e grava, sco üna sgür pronta pel cumbat, o ch'el sta ingramüschà sco ün vegliet cha la burasca da la vita ha fat sgobar sün sias crotschas.

Throughout the last centuries, the structure and genetic composition of forests have been strongly affected by forest management. Over 30% of European forests are artificially regenerated, very often using translocated forest reproductive material, among these species the Swiss stone pine (Pinus cembra L.). In the late nineteenth and early twentieth centuries, the species was largely used for artificial afforestation in the northern Alps. However, only a few planted trees have survived. Therefore, we aimed to evaluate if the historical afforestation of P. cembra in the northwestern Swiss Alps relied on allochthonous material. We sampled 12 sites, genotyping 11 nuclear microsatellites, to infer the spatial genetic structure of regional populations, to test for genetic differences between natural and planted stands, and to infer potential source regions of planted stands using reference samples covering the entire Alps. Population genetic structure analysis allowed us to distinguish planted from natural stands and to determine that forest reproductive material used for plantations was not of regional origin. We found similar levels of genetic diversity between natural and planted stands. Assignment tests revealed that reproductive material for planting was translocated to the study area from two source regions, i.e., near the border of Switzerland and Austria, and further to the East, between Austria and Italy. Our study shows how genetic tools may inform about historical transfer of forest reproductive material, which still may affect the population genetic make-up of regional occurrences, e.g., because of reduced natural regeneration.

We adopted a landscape-scale approach to analyze the genetic patterns (diversity, structure, and differentiation) of the Marbled White (Melanargia galathea). This butterfly species is characteristic of semi-dry grasslands, which have substantially declined in Switzerland during past decades. We sampled individuals on a regular grid of the established Biodiversity Monitoring program of Switzerland over five consecutive years, obtaining 1639 genotyped individuals from 185 locations. Results showed that M. galathea populations cluster into five spatially aggregated clusters that largely coincide with the biogeographic regions of Switzerland. Genetic diversity (allelic richness) was higher in the South of the Alps, likely related to immigration dynamics that suggest recolonisation from the South after the last glaciation. Demographic history resulted in distinct isolation by distance (IBD) and by cumulative elevational difference (isolation by altitude, IBA) at large scale, while regional IBD and IBA were less pronounced. This pattern was likely induced by the barrier effect of the high mountains of the Alps impeding continuous northward migration after the last glacial maximum. A temporal analysis revealed that regional genetic diversity did not change strongly during the five sampling years. This result indicates that the genetic diversity pattern in M. galathea has not been noticeably affected by historical land-use change or that the sampling period of five years is too short to detect any changes. Our findings highlight the regionally, topography-induced distinct genetic clusters, relevant for consideration as conservation units and likely reflecting genetic structures similar to those found in other butterfly species of conservation concern.

Seit Jahrhunderten wachsen einige Riesenarven südlich der Gemeinde Celerina am oberen Waldrand des God Plazzers. Diese urwüchsigen, knorrigen Altarven sind eindrückliche Mahnmale der harten Lebensbedingungen an diesem Standort und erzeugen beim Betrachten Ehrfurcht und Nachdenken. Sie geben seit Langem einige Rätsel auf, die dank neuen Untersuchungen teilweise geklärt werden konnten.

Aim: Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re-colonisation routes.
Location: European Alps and Carpathians.
Taxa: Pinus cembra.
Methods: We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re-colonisation of the current range.
Results: We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re-colonisation.
Main Conclusions: Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in 'cold period' refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene 'warm period' refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species.

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

Klimawandel, Trockenheit, Tannensterben: Forscherinnen und Forscher debattieren über die Zukunftsaussichten der Weisstanne. Jüngste Forschungsergebnisse deuten an, dass diese Baumart grösseres Potenzial hat als oft angenommen.

Background: Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied.
Results: Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs.
Conclusions: The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research.

Une étude conduite sur plusieurs années par des écologues de l’Institut fédéral de recherche WSL montre que les populations de lièvres variables (Lepus timidus) sont soumises à de fortes fluctuations et que les mâles et les femelles n’utilisent pas leur habitat de la même manière. Ces connaissances acquises dans les Alpes de Suisse orientale améliorent la compréhension de l’écologie de cette fascinante espèce sauvage indigène et fournissent des bases importantes pour sa protection dans les Alpes.

Eine mehrjährige Studie von Wildtierökolog:innen der Eidgenössischen Forschungsanstalt WSL zeigt, dass die Bestände von Schneehasen (Lepus timidus) starken Schwankungen unterliegen und dass Häsin und Rammler den Lebensraum unterschiedlich nutzen. Die Erkenntnisse  aus dem Schweizerischen Nationalpark verbessern das Verständnis zur Ökologie dieser faszinierenden einheimischen Wildtierart und liefern wichtige Grundlagen für einen wirkungsvollen Schutz des Schneehasen in den Alpen.

Wenn im Winter die Landschaft weiß gefärbt ist, dann verraten die Spuren im Schnee den gut getarnten und heimlich lebenden Schneehasen. Doch wie groß sind die Bestände in einem Gebiet und wie wird der Lebensraum durch die Hasen genutzt? Diesen Fragen sind Schweizer Wildtierökologen der Eidgenössischen Forschungsanstalt WSL im Rahmen einer mehrjährigen Studie im Schweizerischen Nationalpark nachgegangen. Diese zeigt, dass Schneehasenbestände starken Schwankungen unterliegen und Häsin und Rammler den Lebensraum unterschiedlich nutzen. Diese Erkenntnisse verbessern das Verständnis zur Ökologie dieser faszinierenden einheimischen Wildtierart und liefern wichtige Grundlagen für deren Schutz in den Alpen.

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

It is generally accepted that the spatial distribution of neutral genetic diversity within a species’ native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, F_ST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (H_e) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.

The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species’ long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23 × 10⁻²/generation (i.e. 40 years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96 × 10⁻²/generation) and precipitation (0.91 × 10⁻²/generation). These recent shifts were corroborated by forward-in-time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature-associated loci was decidedly lower than the estimated average rate of 6.29 × 10⁻²/generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.

Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5‐year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex‐specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.

Heimliche Tierarten sind schwer zu beobachten und entsprechend weiss man oft wenig über deren einzelne Vorkommen. Hier bietet das nicht-invasive genetische Monitoring neue Möglichkeiten, um die Bestände von solcher Arten verlässlich zu erfassen und Veränderungen festzustellen. Wir zeigen am Beispiel des Schneehasen im Schweizerischen Nationalpark, wie man die Populationsdynamik einer versteckt lebenden Art mit genetischen Methoden beschreiben kann und welche Erkenntnisse sich daraus ableiten lassen.

Les espèces animales menant une vie discrète sont difficiles à observer et les connaissances relatives à leur présence sont souvent limitées. Le monitoring génétique non invasif offre de nouvelles opportunités pour enregistrer de manière fiable les effectifs de ces espèces et détecter les variations. En prenant l'exemple du lièvre variable dans le Parc national suisse, nous montrons comment il est possible de décrire la dynamique de population d'une espèce vivant cachée en s'appuyant sur des méthodes génétiques, et quelles conclusions il est possible d'en tirer.