Condition-dependent signalling of genetic variation in stalk-eyed flies

Handicap models of sexual selection predict that male sexual ornaments have strong condition-dependent expression and this allows females to evaluate male genetic quality. A number of previous experiments have demonstrated heightened condition-dependence of sexual ornaments in response to environmental stress. Here we show that genetic variation underlies the response to environmental stress (variable food quality) of a sexual ornament (male eye span) in the stalk-eyed fly Cyrtodiopsis dalmanni. Some male genotypes develop large eye span under all conditions, whereas other genotypes progressively reduce eye span as conditions deteriorate. Several non-sexual traits (female eye span, male and female wing length) also show genetic variation in condition-dependent expression, but their genetic response is entirely explained by scaling with body size. In contrast, the male sexual ornament still reveals genetic variation in the response to environmental stress after accounting for differences in body size. These results strongly support the hypothesis that female mate choice yields genetic benefits for offspring.     

Sexually antagonistic genetic variation for fitness in red deer

Evolutionary theory predicts the depletion of genetic variation in natural populations as a result of the effects of selection, but genetic variation is nevertheless abundant for many traits that are under directional or stabilizing selection. Evolutionary geneticists commonly try to explain this paradox with mechanisms that lead to a balance between mutation and selection. However, theoretical predictions of equilibrium genetic variance under mutation-selection balance are usually lower than the observed values, and the reason for this is unknown. The potential role of sexually antagonistic selection in maintaining genetic variation has received little attention in this debate, surprisingly given its potential ubiquity in dioecious organisms. At fitness-related loci, a given genotype may be selected in opposite directions in the two sexes. Such sexually antagonistic selection will reduce the otherwise-expected positive genetic correlation between male and female fitness. Both theory and experimental data suggest that males and females of the same species may have divergent genetic optima, but supporting data from wild populations are still scarce. Here we present evidence for sexually antagonistic fitness variation in a natural population, using data from a long-term study of red deer (Cervus elaphus). We show that male red deer with relatively high fitness fathered, on average, daughters with relatively low fitness. This was due to a negative genetic correlation between estimates of fitness in males and females. In particular, we show that selection favours males that carry low breeding values for female fitness. Our results demonstrate that sexually antagonistic selection can lead to a trade-off between the optimal genotypes for males and females; this mechanism will have profound effects on the operation of selection and the maintenance of genetic variation in natural populations.     

具有局部搜索能力的自适应变异遗传算法

针对函数优化问题，提出一种自适应变异遗传算法来提高局部搜索的能力，弥补简单遗传算法易于早熟收敛的缺陷。最后以De Jong函数为仿真对象，将此算法与其它三种遗传算法进行比较，仿真结果表明此算法对于函数优化问题非常有效，大大加快了算法的收敛速度，并大幅度提高了搜寻到最优解的概率。     

交趾黄檀种源苗期生长性状地理变异和遗传稳定性分析

【目的】交趾黄檀(Dalbergia cochinchinensis)是珍稀红木树种之一,其木材及木制品极为珍贵,亦具有重要的药用价值。为了研究交趾黄檀不同种源的苗木生长差异、种源与环境互作效应、地理变异模式以及遗传稳定性,进行不同种源交趾黄檀苗期生长评价,为交趾黄檀的幼林期试验提供科学指导和理论支持,也为今后进一步开展交趾黄檀优良种源选择和育苗工作奠定基础。【方法】将引种于泰国、柬埔寨交趾黄檀10个种源的种子分别在海南乐东、广东广州和福建漳州进行多点育苗试验,并对1年生的苗木开展苗期生长性状(苗高和地径)测定与分析。用ASReml-R 3.0对种源与试验点进行方差分析,探讨种源间变异水平以及遗传稳定性; 通过种源生长量均值与种子引种地的地理气候因子的简单相关分析揭示交趾黄檀苗期生长的地理变异模式; 应用R语言程序(GGEBiplots)双标图进行各种源表现型及试验点的代表性分析,并采用类平均法进行基于表型的种源系统聚类分析。【结果】①不同种源交趾黄檀在3个试验点中表现一致,平均参试苗木高生长表现最好的是泰国北柳(T-CS)种源,平均地径生长表现最好的是泰国呵叻(T-NR)种源,来自柬埔寨磅湛(C-KC)种源的苗木生长表现最差。②交趾黄檀种源间苗期生长性状具有显著差异,各性状种源×地点具有极显著效应,表明种源、环境、种源×环境互作等效应对交趾黄檀苗木生长性状影响极其显著。③通过不同种源苗木多点生长表现与引种地地理气候因子的相关分析发现,10个种源交趾黄檀的生长性状在地理空间上存在一定程度的连续变异。生长性状的地理变异存在明显的气候生态学特征,主要受经度和年降雨量控制。④通过各种源在3个试验点的GGE双标图分析,泰国北柳(T-CS)种源和柬埔寨暹粒(C-SR)种源在3个试验点表现较优。柬埔寨暹粒(C-SR)种源在3个试验点的生长相对较稳定。⑤根据苗木生长表现、种源及试验点的遗传稳定性和聚类分析的结果,可以将10个种源大致划分为4个类群。生长表现最好的一类种源在苗高和地径上比最差的种源分别提高了147.23%和80.50%。【结论】通过多点多种源的联合分析可知,交趾黄檀在我国南方地区苗期生长良好,尤其适应我国海南热带地区。综合各种源苗木在各试验点的苗期生长表现,初步筛选出泰国北柳(T-CS)和柬埔寨暹粒(C-SR)2个生长表现较优且适应性较强的种源,可在我国南方热带和亚热带地区开展引种和遗传育种工作。     

Organization of genetic variation in individuals of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal (AM) fungi (Glomeromycota) are thought to be the oldest group of asexual multicellular organisms. They colonize the roots of most land plants, where they facilitate mineral uptake from the soil in exchange for plant-assimilated carbon. Cells of AM fungi contain hundreds of nuclei. Unusual polymorphism of ribosomal DNA observed in individual spores of AM fungi inspired a hypothesis that heterokaryosis--that is, the coexistence of many dissimilar nuclei in cells--occurs throughout the AM fungal life history. Here we report a genetic approach to test the hypothesis of heterokaryosis in AM fungi. Our study of the transmission of polymorphic genetic markers in natural isolates of Glomus etunicatum, coupled with direct amplification of rDNA from microdissected nuclei by polymerase chain reaction, supports the alternative hypothesis of homokaryosis, in which nuclei populating AM fungal individuals are genetically uniform. Intrasporal rDNA polymorphism contained in each nucleus signals a relaxation of concerted evolution, a recombination-driven process that is responsible for homogenizing rDNA repeats. Polyploid organization of glomeromycotan genomes could accommodate intranuclear rDNA polymorphism and buffer these apparently asexual organisms against the effects of accumulating mutations.     

Proportionally more deleterious genetic variation in European than in African populations

Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P < 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P < 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.     

Adaptive variation in environmental and genetic sex determination in a fish

Two general mechanisms of sex determination have been identified among gonochoristic vertebrates: environmental sex determination where offspring become male or female in response to an environmental factor(s) during development (for example, some fishes and reptiles); and genetic sex determination where sex is determined by genotype at conception (as in birds and mammals). How do these sex-determining systems evolve? Direct evidence is virtually non-existent because the sex-determining systems of most species appear to have little genetic variation. Here we provide the first evidence of adaptive variation in environmental and genetic sex determination within a species. We show that in a fish with temperature-dependent sex determination, populations at different latitudes compensate for differences in thermal environment and seasonality by adjusting the response of sex ratio to temperature, and by altering the level of environmental as opposed to genetic control. The adjustments observed are precisely those predicted by adaptive sex ratio theory.     

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

Cryptic variation is caused by the robustness of phenotypes to mutations. Cryptic variation has no effect on phenotypes in a given genetic or environmental background, but it can have effects after mutations or environmental change. Because evolutionary adaptation by natural selection requires phenotypic variation, phenotypically revealed cryptic genetic variation may facilitate evolutionary adaptation. This is possible if the cryptic variation happens to be pre-adapted, or "exapted", to a new environment, and is thus advantageous once revealed. However, this facilitating role for cryptic variation has not been proven, partly because most pertinent work focuses on complex phenotypes of whole organisms whose genetic basis is incompletely understood. Here we show that populations of RNA enzymes with accumulated cryptic variation adapt more rapidly to a new substrate than a population without cryptic variation. A detailed analysis of our evolving RNA populations in genotype space shows that cryptic variation allows a population to explore new genotypes that become adaptive only in a new environment. Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution.     

Cryptic simplicity in DNA is a major source of genetic variation

DNA regions which are composed of a single or relatively few short sequence motifs usually in tandem ('pure simple sequences') have been reported in the genomes of diverse species, and have been implicated in a range of functions including gene regulation, signals for gene conversion and recombination, and the replication of telomeres. They are thought to accumulate by DNA slippage and mispairing during replication and recombination or extension of single-strand ends. In order to systematize the range of DNA simplicity and the genetic nature of the regions that are simple, we have undertaken an extensive computer search of the DNA sequence library of the European Molecular Biology Laboratory (EMBL). We show here that nearly all possible simple motifs occur 5-10 times more frequently than equivalent random motifs. Furthermore, a new computer algorithm reveals the widespread occurrence of significantly high levels of a new type of 'cryptic simplicity' in both coding and noncoding DNA. Cryptically simple regions are biased in nucleotide composition and consist of scrambled arrangements of repetitive motifs which differ within and between species. The universal existence of DNA simplicity from monotonous arrays of single motifs to variable permutations of relatively short-lived motifs suggests that ubiquitous slippage-like mechanisms are a major source of genetic variation in all regions of the genome, not predictable by the classical mutation process.     

Palaeoceanographic implications of genetic variation in living North Atlantic Neogloboquadrina pachyderma

The shells of the planktonic foraminifer Neogloboquadrina pachyderma have become a classical tool for reconstructing glacial-interglacial climate conditions in the North Atlantic Ocean. Palaeoceanographers utilize its left- and right-coiling variants, which exhibit a distinctive reciprocal temperature and water mass related shift in faunal abundance both at present and in late Quaternary sediments. Recently discovered cryptic genetic diversity in planktonic foraminifers now poses significant questions for these studies. Here we report genetic evidence demonstrating that the apparent 'single species' shell-based records of right-coiling N. pachyderma used in palaeoceanographic reconstructions contain an alternation in species as environmental factors change. This is reflected in a species-dependent incremental shift in right-coiling N. pachyderma shell calcite delta18O between the Last Glacial Maximum and full Holocene conditions. Guided by the percentage dextral coiling ratio, our findings enhance the use of delta18O records of right-coiling N. pachyderma for future study. They also highlight the need to genetically investigate other important morphospecies to refine their accuracy and reliability as palaeoceanographic proxies.     

TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis

Although there has been much success in identifying genetic variants associated with common diseases using genome-wide association studies (GWAS), it has been difficult to demonstrate which variants are causal and what role they have in disease. Moreover, the modest contribution that these variants make to disease risk has raised questions regarding their medical relevance. Here we have investigated a single nucleotide polymorphism (SNP) in the TNFRSF1A gene, that encodes tumour necrosis factor receptor 1 (TNFR1), which was discovered through GWAS to be associated with multiple sclerosis (MS), but not with other autoimmune conditions such as rheumatoid arthritis, psoriasis and Crohn’s disease. By analysing MS GWAS data in conjunction with the 1000 Genomes Project data we provide genetic evidence that strongly implicates this SNP, rs1800693, as the causal variant in the TNFRSF1A region. We further substantiate this through functional studies showing that the MS risk allele directs expression of a novel, soluble form of TNFR1 that can block TNF. Importantly, TNF-blocking drugs can promote onset or exacerbation of MS, but they have proven highly efficacious in the treatment of autoimmune diseases for which there is no association with rs1800693. This indicates that the clinical experience with these drugs parallels the disease association of rs1800693, and that the MS-associated TNFR1 variant mimics the effect of TNF-blocking drugs. Hence, our study demonstrates that clinical practice can be informed by comparing GWAS across common autoimmune diseases and by investigating the functional consequences of the disease-associated genetic variation.     

煤矿顶板透水事故预测与控制技术

在深入研究我国煤矿顶板透水发生及其成功控制案例的基础上,对顶板透水事故发生的原因、实现的条件及其动力信息基础进行了系统研究,以此为基础提出了顶板透水事故预测与控制的方法.针对淮南矿业集团谢桥煤矿1122(3)工作面,分析了谢桥井田地质及水文地质特征,并根据钻孔及井下资料,研究了顶板砂岩、粉砂岩运动规律.以实用矿山压力控制理论为指导,建立项板控制信息动力决策模型,着重探讨了导水裂隙带和斑裂纹对顶板砂岩透水的影响机理.     

Phase variation in Bordetella pertussis by frameshift mutation in a gene for a novel two-component system

Bordetella pertussis, the aetiological agent of whooping cough, coordinately regulates the expression of many virulence-associated determinants, including filamentous haemagglutinin, pertussis toxin, adenylyl cyclase toxin, dermonecrotic toxin and haemolysin. The coordinate regulation is apparent in the repression of synthesis of these determinants in response to environmental stimuli; a phenomenon known as antigenic or phenotypic modulation. B. pertussis also varies between metastable genetic states, or phases. There is a virulent phase in which virulence-associated determinants are synthesized, and an avirulent phase in which they are not. Previous studies have shown that a genetic locus, vir, is required for expression from many virulence-associated loci, and that replacing the cloned vir locus in trans can restore the virulent phase phenotype to spontaneously occurring avirulent phase strains. Here, we show that phase variation in one series of strains is due to a frameshift mutation within an open reading frame that is predicted to code for a Vir protein product. The deduced protein sequence is similar to both components of the 'two-component' regulatory system which control gene expression in response to environmental stimuli in a range of bacterial species.     

Analysis of the matrilineal genetic structure of population in the early Iron Age from Tarim Basin, Xinjiang, China

Ancient mtDNA data of human remains were analyzed from four early Iron Age Tarim Basin sites （Yuansha, Zaghunluq, Sampula and Niya） in the southern Silk Road region. Haplogroup distributions show that ancient Tarim Basin population was comprised of well-differentiated Western and Eastern matrilineal lineages. Some West lineage of Tarim Basin population originated from Near East and Iran region. Of the East lineages, North and Northeast Asia originated lineages were the main components, and a few Southeast Asian lineages also existed, which indicated a more extensive origin and a more complex admixture. The genetic structure of ancient Tarim Basin population is relatively close to the modern populations of Xinjiang, which implied that the early Iron Age is an important period during the formation of the modern Xinjiang population.     

基于时间序列疏系数模型的太阳辐射年际变化趋势预测

利用1961—2016年山东省济南市太阳年总辐射量观测数据,通过模型识别和统计检验,对比分析时间序列模型AR(5)和ARIMA((1,2,4),1,0)的拟合结果。残差检验结果表明,疏系数模型ARIMA ((1,2,4),1,0)可用于预测地表太阳年总辐射量,预测结果显示2017—2025年济南市地表太阳辐射的年际变化整体呈增长趋势。对比多元线性回归模型结果,时间序列疏系数模型误差较小,预测准确度相对较高。