The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species.

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.

Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions.

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.

Highly polymorphic microsatellite markers in Pulsatilla vulgaris (Ranunculaceae) using next-generation sequencing.

PREMISE OF THE STUDY: We developed novel microsatellite markers for the perennial plant Pulsatilla vulgaris (Ranunculaceae) 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.

Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpina (Brassicaceae).

PREMISE OF THE STUDY: Polymorphic microsatellite markers were developed for the inbred alpine perennial plant Arabis alpine to infer life-history parameters and measure patterns of contemporary gene fl ow 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 amplifi ed di- and trinucleotide repeats with two to fi ve alleles per locus. CONCLUSIONS: Previous attempts to isolate microsatellite loci in A. alpina using enrichment libraries and cross-amplifi cation were diffi cult 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.

Effects of floral neighborhood on seed set and degree of outbreeding in a high-alpine cushion plant.

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 co-flowering 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.

Lower selfing rate at higher altitudes in the alpine plant Eritrichium nanum (Boraginaceae).

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.