René Graf

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.

Botanische Bestimmungsschlüssel sind effiziente Werkzeuge bei der Artbestimmung in der Natur. Sie beruhen aber auf äusseren Merkmalen, die nicht nur von der Artzugehörigkeit, sondern auch von den Umweltbedingungen beeinflusst sind. Ausserdem ignorieren sie meist zwischenartliche Kreuzungen. Diesbezüglich haben genetische Methoden einen Vorteil, sind aber für Praktiker im Feld nicht anwendbar. Hier vergleichen wir die Artbestimmung (inklusive Kreuzungen) mittels Feldschlüssel und Genetik bei den drei häufigsten Eichenarten (Quercus spp.) der Schweiz. Diese Eichen sind schwierig zu bestimmen, weil sie eine grosse blattmorphologische Variabilität aufweisen und sich untereinander kreuzen. Unsere Analyse zeigt, dass die Übereinstimmung der beiden Methoden grundsätzlich gross ist, dass aber insbesondere beim Artenkomplex von Trauben- und Flaumeiche eine gewisse Unschärfe besteht, die sowohl methodisch (z.B. durch Festlegung von Schwellenwerten) wie auch biologisch (z.B. durch phänotypische Plastizität) bedingt sind. Unsere Studie unterstreicht die Wichtigkeit von genetischen Methoden bei der Validierung von Feldschlüsseln und zeigt die potenzielle Rolle von Feldschlüsseln zur Beurteilung der zwischen- und innerartlichen Vielfalt. So können gemischte Bestände und genetisch durchmischte Bäume gefördert werden, die für zukünftige Klimaveränderungen gewappnet sind.

Botanical identification keys are efficient tools in species determination in nature. However, they are based on phenotypic traits that are influenced not only by species identity but also by environmental conditions. Moreover, they usually ignore interspecific hybridization. In this respect, genetic methods have an advantage but are not applicable for practitioners in the field. Here we compare species determinations (including crosses) using an identification key and genetics in the three most common oak species (Quercus spp.) in Switzerland. These oaks are difficult to assign to species because they show great leaf morphological variability and admixture. Our analysis shows a good agreement between the two methods, but there is, especially for the species complex of sessile and downy oak, some uncertainty, due to both methodological (e.g., by setting thresholds) and biological (e.g., by phenotypic plasticity) reasons. Our study highlights the importance of genetic methods in validating identification keys and demonstrates the potential role of identification keys in assessing inter- and intraspecific diversity. This can promote mixed stands and intermixed trees that are resilient to future climate change.

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.

Motivation: Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU‐Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra‐ and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes.
Main types of variable contained: We chose morphological and chemical characters linked to trade‐offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope ¹³C and ¹⁵N in leaves.
Spatial location and grain: We surveyed between 18 and 22 populations per species, 141 in total, across Europe.
Time period: Leaf sampling took place between 2016 and 2017.
Major taxa and level of measurement: We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea.
Software format: The data files are in ASCII text, tab delimited, not compressed.

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.

Die Kirschessigfliege (Drosophila suzukii) ist eine invasive Art, die in Europa eingeschleppt wurde und Schäden in Frucht-Kulturen verursacht. Als vielversprechender einheimischer Parasitoid zur biologischen Bekämpfung von D. suzukii wird Trichopria drosophilae betrachtet. Um die genetische Vielfalt und die räumliche genetische Struktur in Populationen von T. drosophilae zu bestimmen, entwickelten wir 21 neue, für diese Art spezifische molekulare Marker (Mikrosatelliten). Proben von T. drosophilae wurden an 16 Standorten jeweils in drei unterschiedlichen Lebensraumtypen gesammelt und liessen drei genetische Gruppen erkennen. Obwohl viele Individuen eine gemischte Zuordnungswahrscheinlichkeit zu drei genetischen Gruppen aufwiesen, gab es einen Zusammenhang zwischen der Zugehörigkeit zu einer dieser Gruppen und dem bevorzugten Lebensraum (geringer Genfluss zwischen Lebensräumen innerhalb der Standorte). Weitere Analysen deuten an, dass T. drosophilae sich rasch zwischen verschiedenen Regionen ausbreitet (hoher Genfluss zwischen Standorten). Unsere Ergebnisse zeigen, wie genetische Untersuchungen genutzt werden können, um die Ausbreitung von Organismen zur biologischen Schädlingsbekämpfung zu verfolgen.

Glaciation during the Pleistocene confined alpine species to refugial areas. These range contractions had major impacts on the spatial genetic structure of alpine species. Consequently, one should take into account the often complex phylogeographic structure of species when performing genomic research, e.g. on signatures of local adaptation. Understanding the phylogeography of the widespread arctic and alpine Arabis alpina is particularly important, as this species is developing into a model species for ecological genetics. The first objective of this study was to assess the genetic variation of A. alpina across the Alps and to compare the spatial genetic patterns resulting from two different types of molecular markers, namely nuclear microsatellites and amplified fragment length polymorphisms (AFLPs). A second objective was to infer the distribution of genetic variation at the regional scale to understand the genetic structure of populations in the area of a previously suggested contact zone between genetic clusters that presumably recolonised their current range from different glacial refugia. We characterized the phylogeographic structure of 372 individuals from 127 populations across the entire Alpine range, complemented by 364 individuals from 22 populations in the western Swiss Alps. Nuclear microsatellite and AFLP markers described consistent population clustering, coherent with previous phylogeographic analyses. Furthermore, regional population structure in the western Alps of Switzerland highlighted a contact zone of genetic clusters associated with different presumed refugia. Again, this finding was in accordance with recolonisation routes formerly inferred for other plant taxa of the western Swiss Alps. Our results highlight the coincidence of large-scale patterns of genetic structure among alternative types of molecular markers and set a valuable basis for further studies on ecological genomics in A. alpina.

Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations. We analysed new SNP data of 444 plants with the same methodology (partial Mantel tests, PMTs) as in the original study and additionally with a latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41% (PMTs) and 51% (LFMM) were associated with environmental factors in the independent data set. However, only 5% (PMTs) and 15% (LFMM) of the associations showed the same environment–allele relationships as in the original study. In total, we found 11 genes (31%) containing the same association in the original and independent data set. These can be considered prime candidate genes for environmental adaptation at a broader geographical scale. Our results suggest that selection pressures in highly heterogeneous alpine environments vary locally and signatures of selection are likely to be population-specific. Thus, genotype-by-environment interactions underlying adaptation are more heterogeneous and complex than is often assumed, which might represent a problem when testing for adaptation at specific loci.

Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested whether >3500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate and soil characteristics. In the analysis including all species, the most frequently associated environmental factors were those best describing the habitats of the species. In the species-specific analyses, the most important environmental factors and associated SNPs greatly differed among species. However, we identified one SNP and seven genes that were associated with the same environmental factor across all species. We finally used regressions of allele frequencies of the most strongly associated SNPs along environmental gradients to predict the risk of nonadaptedness (RONA), which represents the average change in allele frequency at climate-associated loci theoretically required to match future climatic conditions. RONA is considerable for some populations and species (up to 48% in single populations) and strongly differs among species. Given the long generation time of oaks, some of the required allele frequency changes might not be realistic to achieve based on standing genetic variation. Hence, future adaptedness requires gene flow or planting of individuals carrying beneficial alleles from habitats currently matching future climatic conditions.

· Key message. We show that joint multivariate analyses of leaf morphological characters and molecular-genetic markers improve the taxonomic assignment in hybridizing European white oaks. However, model-based approaches using genetic data alone represent straightforward alternatives to laborious, detailed morphological assessments.
· Context. In European white oaks, species delimitation is debated because of large overlap of morphological characteristics likely due to hybridization.
· Aims. We tested whether joint multivariate analyses of leaf morphology and molecular markers improve the identification of three oak species (Quercus petraea, Quercus pubescens, Quercus robur) compared to approaches using morphological or genetic variables only.
· Methods. We assessed 13 leaf morphological characters and applied eight nuclear microsatellite markers in almost 1400 trees of 71 oak populations across Switzerland. We performed two multivariate approaches with three variable sets (morphology, genetics, combined) and assessed their performance in separating the taxa. We also compared the taxon assignment to a model-based clustering approach (STRUCTURE) based on genetic data alone.
· Results. A joint use of morphological and genetic variables led to an improved taxon assignment. Whereas Q. robur could clearly be separated from the two other taxa, there was a certain overlap between Q. petraea and Q. pubescens. The STRUCTURE clustering led to the same taxon assignment in 85 % of the individuals.
· Conclusion. It is important to consider both morphological and genetic properties in morphologically similar and hybridizing species. However, it might be more efficient to concentrate only on genetic markers than on time-consuming morphological assessments.

Premise of the study: We developed novel microsatellite markers for the perennial plant Pulsatilla (Ranunculacerie) to investigate the effects of fragmentation on gene flow in this imperiled species.
Methods and Results: We identified microsatellites and developed primers based on 454 shotgun sequences. We identified 14 markers that were polymorphic and produced clean bands. Of these, eight could be analyzed as diploids. Genotyping of 97 individuals across two populations revealed these markers to be highly polymorphic with seven to 17 alleles per locus and observed heterozygosity from 0.41 to 0.83.
Conclusions: The markers are highly informative and will be used to test if the reintroduction of shepherding in southern Germany improves genetic connectivity among fragmented populations of P vulgaris. The combination of diploid and tetraploid markers presented here will be useful in resolving the polyploidization history of this and related species.

Sowing with seed mixtures is a common practice in restoring species-rich communities in areas with impoverished species pools. The potential genetic consequences of using these mixtures, however, are poorly understood and often not considered in practical restoration. We investigated genetic diversity, inbreeding and genetic structure of samples collected from 26 populations of the common wetland plant species Lychnis flos-cuculi in an agricultural region in Switzerland. Some of these populations were natural, while others had been sown several years ago. This enabled us to compare the genetic composition of populations of indigenous origin with those originating from commercially produced seed mixtures. Gene diversity and allelic richness were similar in natural and sown populations. In contrast, inbreeding coefficients were three times higher in sown than in natural populations. The sown populations were genetically distinct from the native populations. We distinguished two homogeneous gene pools that presumably originated from different source populations used to produce seed mixtures. The use of commercially produced seeds may alter the genetic diversity and structure of plant populations. The observed higher inbreeding coefficients of sown populations could lead to reduced population viability. To restore genetically diverse populations, the seeds for further propagation should be collected from numerous individuals in large and non-isolated populations nearby restored sites. Ex situ stocks for the production of commercial seed mixtures should only be propagated for a few generations to avoid negative effects such as inbreeding or loss of local adaptation.

Premise of the study: Polymorphic microsatellite markers were developed for the inbred alpine perennial plant Arabis alpina to infer life-history parameters and measure patterns of contemporary gene flow within populations.
Methods and Results: Using the 454 pyrosequencing technique, 19 microsatellite primer sets were developed for A. alpina. The primer sets were tested on 60 individuals sampled from three sub-populations in the Swiss Alps. The primers amplified di- and trinucleotide repeats with two to five alleles per locus.
Conclusions: Previous attempts to isolate microsatellite loci in A. alpina using enrichment libraries and cross-amplification were difficult and produced an insufficient number of polymorphic microsatellite loci. In contrast, next-generation sequencing technology was successful in identifying microsatellite repeats in A. alpina. These newly developed microsatellite primers will be useful to further develop A. alpina into a model species for eco-genomic studies.

Plants flowering together may influence each other’s pollination and fecundity over a range of physical distances. Their effects on one another can be competitive, neutral, or facilitative. We manipulated the floral neighborhood of the high-alpine cushion plant Eritrichium nanum in the Swiss Alps and measured the effects of coflowering neighbors on both the number of seeds produced and the degree of inbreeding and outbreeding in the offspring, as deduced from nuclear microsatellite markers. Seed set of E. nanum did not vary significantly with the presence or absence of two Saxifraga species growing as near neighbors, but it was higher in E. nanum cushions growing at low conspecific density than in those growing at high density. In addition, floral neighborhood had no detectable effect on the degree of selfing of E. nanum, but seeds from cushions growing at low conspecific density were more highly outbred than seeds from cushions at high density. Thus, there was no evidence of either competition or facilitation between E. nanum and Saxifraga spp. as mediated by pollinators at the spatial scale of our experimental manipulation. In contrast, the greater fecundity of E. nanum cushions at low density was consistent with reduced intraspecific competition for pollinators and might also represent a beneficial effect of highly outbred seeds as brought about by more long-distance pollinator flights under low-density conditions.

Seed weight is a prominent life history trait of plants affecting dispersal, establishment, and survival. In alpine environments, the few studies investigating the effect of elevation on seed weight within species have mainly detected a decrease in seed weight with increasing elevation. This relationship is generally attributed to the adverse climate at high elevations. In order to test this hypothesis, we analyzed seed weight variation across altitudes (2,435-3,055 m a.s.l.) in two consecutive years that differed in weather conditions in the high-alpine cushion plant Eritrichium nanum. We found a significant reduction in seed weight with increasing elevation in both years, but in the growing season with more adverse weather conditions, the reduction was more substantial than in the more favorable year. We conclude that alpine plants may be able to produce well-developed seeds at low elevations in almost all years, independent of weather conditions, whereas reproduction through seeds is potentially limited to years of favorable weather at high elevation.

A general hypothesis on mating patterns in alpine plants states that self-fertilization should increase with increasing altitude as a result of pollinator limitation at higher altitudes. However, realized selfing rates under natural conditions, as based on genetic progeny analysis, have not yet been determined for any alpine species across altitude. We therefore assessed the realized selfing rates in about 100 open-pollinated families of the high-alpine cushion plant Eritrichium nanum, sampled along an altitudinal gradient in the Swiss Alps, by using progeny analysis based on six microsatellites. In marked contrast to the general hypothesis, realized selfing rates in E. nanum significantly decreased with increasing altitude, and only progenies from low altitudes were predominantly selfed. However, the higher selfing rates of individuals at lower altitudes could have been caused by unfavorable weather conditions during early growing season when low-elevation plants flowered. In summary, our results on selfing rates in an alpine plant across altitude as well as the results of other studies using experimental hand-pollinations and/or population genetic methods generally do not support the expectation of higher selfing rates at higher altitudes. We therefore ask for further critical examination of realized mating systems in alpine plants.

We characterized eight polymorphic, codominant nuclear microsatellite loci in the tetraploid plant Eritrichium nanum. The different allelic configurations occurring under tetrasomic inheritance were fully resolved at all loci. Two natural populations showed high observed heterozygosities, which were in agreement with Hardy-Weinberg expectations. There was no evidence of genetic linkage disequilibrium for any pair of loci. The results suggest that these microsatellite markers are useful for mating system and population genetic analyses in high-alpine E. nanum.

Der Kastanienrindenkrebs hat sich seit 1986 in vielen Edelkastanienbeständen auf der Alpennordseite ausgebreitet. Bis jetzt gelang es nicht, die Krankheit mit phytosanitären Massnahmen auszumerzen. Die Rindenkrebse können aber mit einem so genannten Hypovirus behandelt werden. Zwischen 2003 und 2005 wurde das Hypovirus in 16 Beständen ausgebracht. Die meisten der behandelten Rindenkrebse heilten aus und vereinzelt wurde auch schon eine selbstständige Ausbreitung des Hypovirus beobachtet.