Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F₁ hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.     

Molecular similarity analysis on biologically active macrocyclic bis(bibenzyls)

Conformational analysis of marchantin A (1), a bis(diarylether) type, and riccardin A (2), a diarylether-biphenyl type macrocyclic bis(bibenzyl) was carried out by systematic unbounded multiple minimum search (SUMM). Mobility of the macrocyclic rings was analysed by variable temperature ¹H-NMR study. Molecular similarity analysis was performed on the minimum energy conformers of 1 and 2 comparing their steric, electrostatic and hydrophobic properties. Correlation between complexation properties and calmodulin inhibitor activity was established. Differences in steric and electrostatic profiles may be responsible for the reduced Ca²⁺ affinity and activity of 2.     

谷子茎尖体外遗传转化体系的建立与优化

以谷子(Seteria italica)豫谷一号为实验材料,建立了一套简便、稳定的体外茎尖遗传转化体系。通过根癌农杆菌(Agrobacterium tumefaciens)介导的茎尖转化法,对转化受体采取不同的处理方式,待拟转化株长到三叶期后进行PCR鉴定。探明了草丁膦(Basta)喷施处理用于谷子转基因幼苗筛选的最适...     

The Usefulness of Various Numerical Methods for Assessing the Specific Effects of Pollution on Aquatic Biota

The data obtained during an extensive multidisciplinary investigation of a polluted harbor basin in Hamburg were analyzed in various ways in order to determine which statistical methods are easiest to interpret and permit the most accurate evaluations. The methods analyzed include the species deficit, index of species similarity, and saprobity index, as well as the more complex cluster and gradient analyses, which revealed a variety of relationships among the biotic communities at the various sampling sites and some ecological tolerance limits of various species. The shortcomings of numerical indices for characterizing water bodies are discussed. It is suggested that biostatistical methods are much more valuable for the empirical evaluation of data than for artificially classifying ecosystems.     

燕山地区白头翁生境伴生植物资源调查与分析

调查与白头翁共存的伴生植物种类、相似性、生活型、分布区类型等,探讨其生态适应性和地理分布规律,针对性地提出白头翁资源保护利用建议,以期为燕山地区白头翁种质资源的保护和利用提供参考。采用访问调查、路线调查和典型样地调查法,对燕山地区白头翁生境伴生植物进行调查与分析。燕山地区从冀东的秦皇岛地区到冀北的承德地区都有白头翁的分布,多生于向阳的山地草坡上,喜光、耐旱、适于阳生性环境。白头翁生境伴生植物共56科128属164种,主要优势科为菊科（Compositae）、豆科（Leguminosae）、禾本科（Gramineae）、蔷薇科（Rosaceae）、唇形科（Labiatae）、百合科（Liliaceae）、毛茛科（Ranunculaceae）、萝藦科（Asclepiadaceae）等,其中乔木共5科5属7种,灌木共22科38属46种,草本植物共35科85属111种。调查的各样地间相似系数普遍较低,说明燕山地区不同地区白头翁生境差别较大,其伴生植物具有多样性的特点。伴生植物属的分布区类型可分为14个,群落具有明显温带性质。燕山地区白头翁生境多样性及伴生植物的多样性,反映出燕山地区白头翁生态适...     

Revisiting the notion of deleterious sweeps

It has previously been shown that, conditional on its fixation, the time to fixation of a semi-dominant deleterious autosomal mutation in a randomly mating population is the same as that of an advantageous mutation. This result implies that deleterious mutations could generate selective sweep-like effects. Although their fixation probabilities greatly differ, the much larger input of deleterious relative to beneficial mutations suggests that this phenomenon could be important. We here examine how the fixation of mildly deleterious mutations affects levels and patterns of polymorphism at linked sites—both in the presence and absence of interference amongst deleterious mutations—and how this class of sites may contribute to divergence between-populations and species. We find that, while deleterious fixations are unlikely to represent a significant proportion of outliers in polymorphism-based genomic scans within populations, minor shifts in the frequencies of deleterious mutations can influence the proportions of private variants and the value of F_ST after a recent population split. As sites subject to deleterious mutations are necessarily found in functional genomic regions, interpretations in terms of recurrent positive selection may require reconsideration.     

Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.     

Meteorological and Hydrographical Features of Vellayani Lake,Kerala, India

Meteorological, physical and chemical parameters of Vellayani Lake, Kerala, India, have been analysed for twelve months (August 1980 to July 1981), the topography of the lake is described, and correlation coefficients were calculated between meteorological and hydrographical parameters. The results indicate that the lake can be converted into a productive aquafarm by means of slight manuring.     

Evidence that presynaptic changes are involved in the expression of LTP and LTD of NMDA receptor-mediated EPSCs in area CA1 of the hippocampus

Plasticity of NMDA receptor-mediated synaptic transmission was studied in the CA1 region of the hippocampus utilising whole cell patch-clamp recording techniques. LTP was associated with a decrease in CV whereas LTD was accompanied by an increase in CV and a decrease in Pr. These data are consistent with LTP and LTD being an opposite expression of the same fundamental process.     

Genetic association study of intron variants in the forkhead box protein P3 gene in Chinese patients diagnosed with cervical cancer

The aim of this study was to investigate the effects of forkhead box protein P3 (FOXP3) intron single nucleotide variants (SNVs) in high‐risk human papilloma virus (HR‐HPV) infection and cervical cancer (CC) malignant lesions. We performed FOXP3 genotyping in 350 patients with CC and 350 healthy controls using the ImLDR multiple single nucleotide polymorphism genotyping technology. The heterozygous mutation TC in rs2294021 decreased the risk of HR‐HPV infection and CC malignant lesions (TC vs. TT: OR = 0.71, 95% CI = 0.51–0.99); the dominant model TC+CC and allele C in rs2294021 decreased the risk of CC malignant lesions (TC+CC vs. TT: OR = 0.69, 95% CI = 0.50–0.95; C vs. T: OR = 0.78, 95% CI = 0.63–0.97). The heterozygous mutation GA, dominant model GA+AA and allele A in rs3761549 also decreased the risk of HR‐HPV infection and CC malignant lesions (GA vs. GG: OR = 0.70, 95% CI = 0.51–0.96; GA+AA vs. GG: OR = 0.69, 95% CI = 0.51–0.94; A vs. G: OR = 0.75, 95% CI = 0.58–0.96). Patients with CC and HR‐HPV infection carrying rs2294021 TC and rs3761549 GA had lower expression of FOXP3 protein. Haplotype analysis revealed that T‐C‐A decreased the risk of HR‐HPV infection. Furthermore, we found a significant association between immune cells infiltration and prognosis in patients with CC. Our findings demonstrated that rs2294021 and rs3761549 variants may protect against HR‐HPV and CC malignant lesions by downregulating FOXP3 and that FOXP3 was associated with immune cells infiltration, which affected the prognosis of CC.