The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios

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

Between but not within species variation in the distribution of fitness effects

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, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised 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 there being 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 that evolutionarily recent events, such as demographic changes and local adaptation, have little impact

C++ code of the SGCS computer program to infer viability selection coefficients using sequential random genotypic samples drawn from a genetic cohort mortality study

The SGCS program implements a quasi-exact neutrality test and a Bayesian method to infer stage-specific viability selection coefficients using sequential random genotypic samples drawn from a longitudinal cohort mortality study, within a generation. An executable file for Windows OS, along with the user manual and test data sets will be available at https://sites.google.com/site/jjrobledo2/softwar

SNP genotypes of naturally established seedlings in Pinus pinaster at Fuencaliente (Ciudad Real, Spain)

One column per individual genotype, comprising 356 diploid SNP loci. The two alleles at each locus are listed together in one column. Missing data coded with hyphens. Seedling samples collected in the field where found over the entire population at three sequential times: "R1" (November 2010), "R2" (March 2011) and "R3" (July 2011). DNA extracted with Invisorb DNA Plant HTS 96 Kit. Genotyped with an oligo pool assay including a selection of 384 SNPs using the Illumina VeraCode platform (see Table S2 in Budde et al. 2014 New Phytologist 201:230-241 for details about the assay and the candidate genes involved)

Data from: Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations

Afforestation is a common and widespread management practice throughout the world, yet its implications for the genetic diversity of native populations are still poorly understood. We examined the effect of Aleppo pine (Pinus halepensis) plantations on the genetic composition of nearby conspecific native populations. We focused on two native populations in Israel with different levels of isolation from the surrounding plantations and compared the genetic diversity of naturally established young trees within the native populations with that of local native adults, using nine nuclear microsatellite markers. We found that the genetic composition of the recruits was significantly different from that of local adults in both populations, with allelic frequency changes between generations that could not be ascribed to random drift, but rather to substantial gene flow from the surrounding planted Aleppo pine populations. The more isolated population experienced a lower gene flow level (22%) than the less isolated population (49%). The genetic divergence between native populations at the adult-tree stage (Fst = 0.32) was more than twice as high as that of the young trees naturally established around native adults (Fst = 0.15). Our findings provide evidence for a rapid genetic homogenization process of native populations following the massive planting efforts in the last decades. These findings have important implications for forest management and nature conservation and constitute a warning sign for the risk of translocation of biota for local biodiversity

A New Method of Estimating the Pollen Dispersal Curve Independently of Effective Density

We introduce a novel indirect method of estimating the pollen dispersal curve from mother–offspring genotypic data. Unlike an earlier indirect approach (TwoGener), this method is based on a normalized measure of correlated paternity between female pairs whose expectation does not explicitly depend on the unknown effective male population density (d(e)). We investigate the statistical properties of the new method, by comparison with those of TwoGener, considering the sensitivity to reductions of d(e), relative to census density, resulting from unequal male fecundity and asynchronous flowering. Our main results are: (i) it is possible to obtain reliable estimates of the average distance of pollen dispersal, δ, from indirect methods, even under nonuniform male fecundity and variable flowering phenology; (ii) the new method yields more accurate and more precise δ-estimates than TwoGener under a wide range of sampling and flowering scenarios; and (iii) TwoGener can be used to obtain approximate d(e) estimates, if needed for other purposes. Our results also show that accurately estimating the shape of the tail of the pollen dispersal function by means of indirect methods remains a very difficult challenge

POLDISP: a software package for indirect estimation of contemporary pollen dispersal

International audiencePOLDSIP 1.0 is a free software package to estimate the distribution of pollen dispersal distances from mother-offspring diploid genotypic data. It requires the spatial coordinates and genotypes of a sample of seed plants and their respective maternal progenies, providing estimates of the average, variance and kurtosis of the pollen dispersal curve. POLDSIP also estimates the effective reproductive density of pollen donors and the correlation of paternity within and among maternal sibships. POLDSIP is useful for characterizing the spatial scale of pollen dispersal, for assessing the variation in male fertility and for investigating biological factors affecting correlated paternity in plants

Nuclear and chloroplast microsatellite genotypes for Pinus sylvestris at Sierra Nevada (Granada, Spain)

One line per combined nuclear-chloroplast individual genotype, comprising 10 nSSR diploid loci and 7 cpSSR haploid regions. For nSSR, the two alleles at each locus are listed in consecutive columns. Missing data coded with zeros. Needle samples collected in the field. DNA extracted with Invisorb DNA Plant HTS 96 Kit. Electrophoresis of amplified products with LI-COR 4300 DNA Analyzer for cpSSRs, and 3130xL and 3500 Genetic Analyzers (Applied Biosystems) for nSSRs. Fragment size determination through visual inspection using external size markers and reference samples with known allele size for cpSSR, and internal size standard and GeneMapper software (Applied Biosystems) for nSSR