abc: an R package for Approximate Bayesian Computation (ABC)

Many recent statistical applications involve inference under complex models, where it is computationally prohibitive to calculate likelihoods but possible to simulate data. Approximate Bayesian Computation (ABC) is devoted to these complex models because it bypasses evaluations of the likelihood function using comparisons between observed and simulated summary statistics. We introduce the R abc package that implements several ABC algorithms for performing parameter estimation and model selection. In particular, the recently developed non-linear heteroscedastic regression methods for ABC are implemented. The abc package also includes a cross-validation tool for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities when performing model selection. The main functions are accompanied by appropriate summary and plotting tools. Considering an example of demographic inference with population genetics data, we show the potential of the R package. R is already widely used in bioinformatics and several fields of biology. The R abc package will make the ABC algorithms available to the large number of R users. abc is a freely available R package under the GPL license, and it can be downloaded at http://cran.r-project.org/web/packages/abc/index.html

Statistical inference in population genetics using microsatellites

Statistical inference from molecular population genetic data is currently a very active area of research for two main reasons. First, in the past two decades an enormous amount of molecular genetic data have been produced and the amount of data is expected to grow even more in the future. Second, drawing inferences about complex population genetics problems, for example understanding the demographic and genetic factors that shaped modern populations, poses a serious statistical challenge. Amongst the many different kinds of genetic data that have appeared in the past two decades, the highly polymorphic microsatellites have played an important role. Microsatellites revolutionized the population genetics of natural populations, and were the initial tool for linkage mapping in humans and other model organisms. Despite their important role, and extensive use, the evolutionary dynamics of microsatellites are still not fully understood, and their statistical methods are often underdeveloped and do not adequately model microsatellite evolution. In this thesis, I address some aspects of this problem by assessing the performance of existing statistical tools, and developing some new ones. My work encompasses a range of statistical methods from simple hypothesis testing to more recent, complex computational statistical tools. This thesis consists of four main topics. First, I review the statistical methods that have been developed for microsatellites in population genetics applications. I review the different models of the microsatellite mutation process, and ask which models are the most supported by data, and how models were incorporated into statistical methods. I also present estimates of mutation parameters for several species based on published data. Second, I evaluate the performance of estimators of genetic relatedness using real data from five vertebrate populations. I demonstrate that the overall performance of marker-based pairwise relatedness estimators mainly depends on the population relatedness composition and may only be improved by the marker data quality within the limits of the population relatedness composition. Third, I investigate the different null hypotheses that may be used to test for independence between loci. Using simulations I show that testing for statistical independence (i.e. zero linkage disequilibrium, LD) is difficult to interpret in most cases, and instead a null hypothesis should be tested, which accounts for the “background LD” due to finite population size. I investigate the utility of a novel approximate testing procedure to circumvent this problem, and illustrate its use on a real data set from red deer. Fourth, I explore the utility of Approximate Bayesian Computation, inference based on summary statistics, to estimate demographic parameters from admixed populations. Assuming a simple demographic model, I show that the choice of summary statistics greatly influences the quality of the estimation, and that different parameters are better estimated with different summary statistics. Most importantly, I show how the estimation of most admixture parameters can be considerably improved via the use of linkage disequilibrium statistics from microsatellite data

Discerning Oriental from European beech by leaf spectroscopy: Operational and physiological implications

European beech (Fagus sylvatica L.) forests have recently experienced severe diebacks that are expected to increase in future. Oriental beech (Fagus sylvatica spp. orientalis (Lipsky) Greut. & Burd) is a potential candidate for assisted migration (AM) in European forests due to its greater genetic diversity and potentially higher drought resistance. Yet AM entails not only benefits, but also risks, and it is therefore important to monitor the progression of introduced (sub)species. Here, we demonstrate the potential of leaf spectroscopy to replace resourceintensive genetic analysis and field phenotyping for the discrimination and characterization of these two beech subspecies. We studied two European beech forests, one in France and one in Switzerland, where Oriental beech from the Greater Caucasus was introduced over 100 years ago. During two summers (2021, 2022), we measured leaf spectral reflectance, leaf morphological and biochemical traits from genotyped adult trees. Subspecies prediction models were developed separately for top-of-canopy leaves (amenable to remote sensing) and bottom-of-canopy leaves (easier to harvest) using partial least squares discriminant analysis (PLS-DA) and different sets of spectral predictors. Morphological, biochemical and spectra-derived leaf traits indicated that Oriental beech trees at the sites studied were characterized by higher lignin and nitrogen per unit leaf area than European beech, suggesting more protein-rich leaves on a per-area basis. The model based on top-of-canopy leaf reflectance spectra in the short-wave-infrared region (SWIR I: 1450–1750 nm) most accurately distinguished Oriental from European beech (BA = 0.86 ± 0.08, k = 0.72 ± 0.15), closely followed by models based on SWIR II, and on spectra-derived traits (BA ≥ 0.84, k ≥ 0.67). This study provides a proof-of-principle for the development of spectroscopy-based approaches when monitoring introduced species, subspecies or provenances. Our findings hold promise for upscaling to large forest areas using airborne remote sensing

Characteristics and regulation of anthocyanin biosynthesis in pepper - review

Pepper is an important horticultural crop due to its culinary as well as ornamental applications. Some Capsicum varieties build up anthocyanins in their different organs. The biosynthesis of these pigments – beside genetic determinism – depends on diverse factors such as the environment, developmental stage and type of tissue. Though anthocyanin biosynthetic pathway has been first described in the 1800s and from then on it has been well established even in species belonging to Solenaceae , information on the pathway is scarce in case of Capsicum spp. This review comprises the current knowledge on the biochemistry and molecular biology of the anthocyanin biosynthetic pathway

Phylogenetic analysis of Tomato spotted wilt virus (TSWV) NSs protein demonstrates the isolated emergence of resistance-breaking strains in pepper

Resurgence of Tomato spotted wilt virus (TSWV) worldwide as well as in Hungary causing heavy economic losses directed the attention to the factors con- tributing to the outbreak of this serious epidemics. The introgression of Tsw resistance gene into various pepper cultivars seemed to solve TSWV control, but widely used resistant pepper cultivars bearing the same, unique resis- tance locus evoked the rapid emergence of resistance- breaking (RB) TSWV strains. In Hungary, the sporadic appearance of RB strains in pepper-producing region was first observed in 2010–2011, but in 2012 it was detected frequently. Previously, the non-structural protein (NSs) encoded by small RNA (S RNA) of TSWV was verified as the avirulence factor for Tsw resistance, therefore we analyzed the S RNA of the Hungarian RB and wild type (WT) isolates and compared to previously analyzed TSWV strains with RB properties from different geographical origins. Phylogenetic analysis demonstrated that the dif- ferent RB strains had the closest relationship with the local WT isolates and there is no conserved mutation present in all the NSs genes of RB isolates from different geograph- ical origins. According to these results, we concluded that the RB isolates evolved separately in geographic point of view, and also according to the RB mechanism

A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia

Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (Fagus sylvatica L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (He) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min–max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species

Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations

Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multi-locus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene-level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes Factors over many possible phase reconstructions. Epistatic selection offers a realistic multi-locus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Over all populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a non-synonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low-elevations and northern or southern populations. Several haplotypes contained non-synonymous mutations situated in genes with known functional importance for adaptation to climatic factor