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Altitudinal gradients represent short-range clines of environmental parameters like temperature, radiation, seasonality and pathogen abundance, which allows to study the footprints of natural selection in geographically close populations. We investigated phenotypic variation for frost resistance and light response in fiveArabidopsis thalianapopulations ranging from 580 to 2,350 meters altitude at two different valleys in the North Italian Alps. All populations were resequenced as pools and we used a Bayesian method to detect correlations between allele frequencies and altitude while accounting for sampling, pooled sequencing and the expected amount of shared drift among populations. The among population variation to frost resistance was not correlated with altitude. An anthocyanin deficiency causing a high leaf mortality was present in the highest population, which may be non-adaptive and potentially deleterious phenotypic variation. The genomic analysis revealed that the two high-altitude populations are more closely related than the geographically close low-altitude populations. A correlation of genetic variation with altitude revealed an enrichment of highly differentiated SNPs located in genes that are associated with biological processes like response to stress and light. We further identified regions with long blocks of presence absence variation suggesting a sweep-like pattern across populations. Our analysis indicate a complex interplay of local adaptation and a demographic history that was influenced by glaciation cycles and/or rapid seed dispersal by animals or other forces.

Hunters and Farmers The Neolithic period in Europe saw the transition from a hunter-gatherer lifestyle to farming. Previous genetic analyses have suggested that hunter-gatherers were replaced by immigrant farmers. Skoglund et al. (p. 747 , published online 24 April) sequenced one Mesolithic and nine Neolithic Swedish individuals to examine the transition from hunter-gatherers to farmers. Substantial genetic differentiation was observed between hunter-gatherers and farmers: There was lower genetic diversity within the hunter-gatherers and gene flow from the hunter-gatherers into the farmers but not vice versa.

Unreduced prolamin fractions of eu- and alloplasmatic octoploid triticale forms were investigated by means of gel electrophoresis. The electrophoretic separation of the prolamin fractions was carried out by using one-dimensional, horizontal, native acidic polyacrylamide gel electrophoresis (APAGE) and gradient gels. A comparison of the electropherogram patterns of triticale forms with those of the genome donors showed that most of the parent prolamins can be found again in the corresponding triticale. However, the bands of the triticale forms exhibited lower intensities than those of the genome donors. On average the gliadin bands of the triticale forms showed equal reductions in intensities, thereby preserving the relationships of the band intensities in most cases. On the other hand, secalin bands which came from the rye parent showed varying reductions in intensities. A comparative analysis of the band patterns revealed that differences could often be found between triticale forms with the same genomic constitution. Often it concerned differences in intensity. In some cases the bands showed changes in mobility or a splitting up into two sub-bands. Starting with the plant material presented here we developed a new nomenclature of the prolamin band patterns of the triticale forms.

Seed proteins of 28 spelt cultivars (Triticum spelta L.), 16 cross combinations between spelt forms or between spelt and English winter wheat cultivars, and ten winter wheat varieties (Triticum aestivum L.) were analysed by SDS (sodium dodecyl sulphate)-PAGE (polyacrylamide-gel electrophoresis). Different wheat types were chosen for distinct purposes: five popular German wheat cultivars were used for a comparison of wheat and spelt protein band patterns, two of them are old varieties (‘Kanzler’ and ‘Jubilar’) and one is a modern wheat standard (‘Orestis’); five English winter wheat varieties with short straw were used for the crosses with spelt cultivars to improve seed yield and especially the lodging resistance of spelt. The objectives of these studies were the adaptation of existing SDS-PAGE methods, which have been successfully applied in other crops, for the analysis of seed proteins in spelt, and the characterization and differentiation of spelt varieties from corresponding cross combinations with other spelt forms or with winter wheat cultivars using gel-electrophoretic methods (SDS-PAGE). Considerable differences in protein band patterns were found between spelt and winter wheat varieties, especially in three distinct lanes of the electropherogrammes where the molecular weights range from 40 to 49 , 53 to 62 and 74 to 115 kDa. Spelt cross combinations, and especially crosses between spelt and winter wheat cultivars, were easily distinguishable particularly after a preceding extraction in chlorethanol.

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns, and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of `standardized allele frequencies' that allows investigators to apply tests of their choice to multiple populations, while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to calculate powerful tests to detect non-parametric correlations with environmental variables, which are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST but should be more powerful as we account for population history. We also extend the model to next-generation sequencing of population pools, which is a cost-efficient way to estimate population allele frequencies, but it implies an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by re-analyzing human SNP data from the HGDP populations. An implementation of our method will be available from http://gcbias.org., 27 pages, 7 figures

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter-mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.

Recent technological progress has permitted the efficient performance of genome-wide association studies (GWAS) to map genetic variants associated with common diseases. Here, we analyzed 2,893 single nucleotide polymorphisms (SNPs) that have been identified in 593 published GWAS as associated with a disease phenotype with respect to their genomic location. In absolute numbers, most significant SNPs are located in intergenic regions and introns. When compared to their representation on the chips, there is essentially overrepresentation of nonsynonymous coding SNPs (nsSNPs), synonymous coding SNPs, and SNPs in untranscribed regions upstream of genes among the disease associated SNPs. A Gene Ontology term analysis showed that genes putatively causing a phenotype often code for membrane associated proteins or signal transduction genes.

Kornvergroserung und Desaktivierung von Fe2O3 verlauft unter sonst gleichen Bedingungen in Stickstoff rascher als in Sauerstoff. Dabei ist der Unterschied unterhalb 950°C nur gering und quantitativer Art, wahrend oberhalb dieser Temperatur ein qualitativer Unterschied im Verlauf der Desaktivierung festzustellen ist.

Background The increasing amount of genome information allows us to address various questions regarding the molecular evolution and population genetics of different species. Such genome-wide data sets including thousands of individuals genotyped at hundreds of thousands of markers require time-efficient and powerful analysis methods. Demography and sampling introduce a bias into present population genetic tests of natural selection, which may confound results. Thus, a modification of test statistics is necessary to introduce time-efficient and unbiased analysis methods. Results We present an improved haplotype-based test of selective sweeps in samples of unequally related individuals. For this purpose, we modified existing tests by weighting the contribution of each individual based on its uniqueness in the entire sample. In contrast to previous tests, this modified test is feasible even for large genome-wide data sets of multiple individuals. We utilize coalescent simulations to estimate the sensitivity of such haplotype-based test statistics to complex demographic scenarios, such as population structure, population growth and bottlenecks. The analysis of empirical data from humans reveals different results compared to previous tests. Additionally, we show that our statistic is applicable to empirical data from Arabidopsis thaliana. Overall, the modified test leads to a slight but significant increase of power to detect selective sweeps among all demographic scenarios. Conclusions The concept of this modification might be applied to other statistics in population genetics to reduce the intrinsic bias of demography and sampling. Additionally, the combination of different test statistics may further improve the performance of tests for natural selection.

Background There is a great interest in understanding the genetic architecture of complex traits in natural populations. Genome-wide association studies (GWAS) are becoming routine in human, animal and plant genetics to understand the connection between naturally occurring genotypic and phenotypic variation. Coalescent simulations are commonly used in population genetics to simulate genotypes under different parameters and demographic models. Results Here, we present phenosim, a software to add a phenotype to genotypes generated in time-efficient coalescent simulations. Both qualitative and quantitative phenotypes can be generated and it is possible to partition phenotypic variation between additive effects and epistatic interactions between causal variants. The output formats of phenosim are directly usable as input for different GWAS tools. The applicability of phenosim is shown by simulating a genome-wide association study in Arabidopsis thaliana. Conclusions By using the coalescent approach to generate genotypes and phenosim to add phenotypes, the data sets can be used to assess the influence of various factors such as demography, genetic architecture or selection on the statistical power of association methods to detect causal genetic variants under a wide variety of population genetic scenarios. phenosim is freely available from the authors' website http://evoplant.uni-hohenheim.de

Background Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits. Results A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait. Conclusions We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.