Genetic structure and population dynamics of a heteroecious plant pathogen Melampsora larici-epitea in short-rotation coppice willow plantations

Complex life strategies are common among plant pathogens belonging to rust fungi ( Uredinales ). The heteroecious willow rust Melampsora larici-epitea produces five spore stages and alternates on larch ( Larix ). To shed light on the epidemiology of this pathogen, amplified fragment length polymorphisms (AFLPs) were used to determine the genetic diversity and genetic structure of rust samples collected from coppice willow ( Salix ) plantations at three UK sites (LA, CA and MC) over three sampling dates (September 2000, July 2001 and September 2001). Of the total of 819 isolates, 465 were unique AFLP phenotypes and there was a shift in genotype diversity between the two seasons (0.67 in 2000 and 0.87–0.89 in 2001). No phenotypes were common between the two seasons within a site, suggesting that the rust did not overwinter as an asexual stage within plantations. A temporal analysis detected large amounts of genetic drift ( F _S = 0.15–0.26) between the two seasons and very small effective population sizes ( N _e  =  2–3) within sites. These results all point to a new colonization of the plantations by the rust in the second season (2001). The F _ST-analogue values were Φ_CT = 0.121, Weir and Cockerham's θ = 0.086 and the Bayesian estimate θ^B = 0.087–0.096. The results suggest that the sources of inoculum were somewhat localized and the same sources were mainly responsible for disease epidemics in LA and CA over the two seasons. The relatively low F _ST-values among sites (0.055–0.13) suggest the existence of significant gene flow among the three sampled sites.     

Characterization of pharmacogenetically relevant CYP2D6 and ABCB1 gene polymorphisms in a Portuguese population sample

Differences in metabolism of drugs can lead to severe toxicity or therapeutic failure. In addition to cytochrome P450 2D6, which plays a critical role in drug metabolism, ABCB1 encoded P‐glycoprotein (PGP) is also an important determinant in drug bioavailability. The genes encoding these molecules are highly variable among populations and, given their clinical importance in drug therapy, determining CYP2D6 and ABCB1 allele frequencies in specific populations is very important for useful application in clinical settings. In this study the frequency of the pharmacologically relevant CYP2D6*3, *4, *5, *6 allelic variants and gene duplication, and ABCB1 C1236T and C3435T gene polymorphisms and their haplotypes was determined in a population sample of 100 Portuguese healthy subjects. CYP2D6 allele frequencies were 1.4% (*3), 13.3% (*4), 2.8% (*5), 1.8% (*6) and 6.1% (gene duplication), with 5% of the individuals classified as PM and 8.4% as UM. The frequencies obtained for the non‐functional alleles and for the CYP2D6 gene duplication are in agreement with other South European populations, and reinforce the previously suggested south/north gradient of CYP2D6 duplications. Allelic frequencies for the ABCB1 polymorphisms were 52% (3435C) and 54% (1236C) and the most common haplotype (1236C‐3435C) occurred with a frequency of 45.5%. Although allele and haplotype frequency data for ABCB1 in Southern Europe is limited, some discrepancies were found with other European populations, with possible therapeutic implications for PGP substrate drugs. Copyright © 2009 John Wiley & Sons, Ltd.     

Allele fixation in a dynamic metapopulation: Founder effects vs refuge effects

The fixation of mutant alleles has been studied with models assuming various spatial population structures. In these models, the structure of the metapopulation that we call the “landscape” (number, size and connectivity of subpopulations) is often static. However, natural populations are subject to repetitive population size variations, fragmentation and secondary contacts at different spatiotemporal scales due to geological, climatic and ecological processes. In this paper, we examine how such dynamic landscapes can alter mutant fixation probability and time to fixation. We consider three stochastic landscape dynamics: (i) the population is subject to repetitive bottlenecks, (ii) to the repeated alternation of fragmentation and fusion of demes with a constant population carrying capacity, (iii) idem with a variable carrying capacity. We show by deriving a variance, a coalescent and a harmonic mean population effective size, and with simulations that these landscape dynamics generate repetitive founder effects which counteract selection, thereby decreasing the fixation probability of an advantageous mutant but accelerate fixation when it occurs. For models (ii) and (iii), we also highlight an antagonistic “refuge effect” which can strongly delay mutant fixation. The predominance of either founder effects or refuge effects determines the time to fixation and mainly depends on the characteristic time scales of the landscape dynamics.     

昆虫质型多角体病毒同义密码子使用模式分析

昆虫质型多角体病毒(cypovirus,CPV)是害虫种群重要调节因子,可用作生物防治剂。本研究采用多元统计分析方法对7种CPV进行密码子使用模式分析,结果表明:CPV密码子使用偏好性较弱,多数基因密码子使用模式受碱基组成影响,少数基因密码子使用模式除碱基组成外还有其它影响因素;中性绘图分析表明碱基组成主要受选择压力影响,受突变影响较小。同一电泳型CPV之间比同一宿主CPV之间共有的偏好性密码子多。CPV基因组内10个基因组片段之间密码子偏好性存在差异。CPV密码子偏好性与宿主昆虫密码子偏好性存在差异,所有CPV与其宿主昆虫共有的偏好性密码子均较少。对应分析进一步证明碱基组成是影响密码子使用的主要因素,不同电泳型CPV具有不同的密码子使用模式。聚类分析表明同一电泳型CPV密码子使用模式相似,同一宿主CPV密码子使用模式差异较大。     

HLA-B*2736等位基因的序列分析

使用FLOW-SSO、PCR-SSP以及测序等分型技术, 发现一个与HLA-B*270401基因相关的未知基因。设计基因特异性引物单独扩增B*27基因的外显子2-5, 包括内含子2-4, 并进行双向测序, 分析与B*270401基因序列的差异。该基因的扩增产物为1 815 bp。与B*270401相比在外显子3和4共有10个碱基的改变, 从而使相应氨基酸发生错义或同义突变。碱基634 A→C (密码子130丝氨酸→精氨酸); 670 A→T (密码子142苏氨酸→丝氨酸); 683 G→T (密码子146色氨酸→亮氨酸); 698 A→T (密码子151谷氨酸→缬氨酸); 774 G→C (密码子176谷氨酸→天冬氨酸); 776 C→A (密码子177苏氨酸→赖氨酸); 781 C→G (密码子179谷氨酰胺→谷氨酸); 789 G→T (密码子181丙氨酸同义突变); 1 438 C→T (密码子206甘氨酸同义突变); 1 449 G→C (密码子210甘氨酸→丙氨酸)。在IMGT/HLA数据库中B*27组只有3个基因（B*270502 / 2706 / 2732）提交了内含子序列。该未知基因的内含子2序列与B*2706相同, 显示了与B*27组基因的同源性, 但其同源性在内含子3、4均未得到支持, 与B*27组基因相比, 内含子3的第106个碱基C→G, 碱基168缺失, 碱基179 G→A, 碱基536 G→A; 内含子4中碱基82 T→C。但其内含子3、4序列却与B*070201完全相同。该基因序列已提交GenBank, 编号为被DQ915176, 被WHO确认为HLA-B*2736等位基因。     

群落均匀度分形分析

修正了Frontier和Ricotta等关于有效物种丰富度指数A与物种丰富度指数S之间幂律关系的定义．探讨了A与S之间分形关系的生态学意义．认为分形维数D是群落均匀度测度值在物种数S不断增加的过程中．向其逼近的一个理论值;提出了利用双对数坐标上建立的A与S拟合直线的方程．对群落均匀度的4种变化趋势进行描述的方法。以广东黑石顶自然保护区森林演替系列为例．研究了针阔叶混交林和常绿阔叶林样带上．随着样带观察长度的逐渐增加群落均匀度的变化情况。结果表明．230m长的混交林样带只存在一个线性无标度区间．群落均匀度随样带长度的不断增加而逐渐降低．向分形维数D=0．810趋近。170m长的常绿阔叶林样带存在两个线性无标度区问．在0～25m的尺度域内．随着样带长度的逐渐增加均匀度不断降低．向分形维数D=0．525逼近;在30～170m的尺度域内．随着样带观察长度的增加．群落均匀度也逐渐增加．向分形维数D=0．920趋近。     

灰飞虱发育起点温度及有效积温的探讨

利用培养箱在恒温条件下饲养灰飞虱Laodelphax striatellus Fallén,测定了卵、若虫、成虫繁殖前和全世代发育历期,用直线回归法计算了灰飞虱各虫态和全世代的发育起点温度和有效积温分别为10.06、6.43、10.29、8.08℃和102.3、365.2、87.5、552.1日·度。并根据有效积温法则预测了该虫在济宁市1年完成的代数为4～5代。     

Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus)

Gene flow and drift shape the distribution of neutral genetic diversity in metapopulations, but their local rates are difficult to quantify. To identify gene flow between demes as distinct from individual migration, we present a modified Bayesian method to genetically test for descendants between an immigrant and a resident in a nonmigratory life stage. Applied to a metapopulation of pond-breeding European newts (Triturus cristatus, T. marmoratus) in western France, the evidence for gene flow was usually asymmetric and, for demes of known census size (N), translated into maximally seven reproducing immigrants. Temporal sampling also enabled the joint estimation of the effective demic population size (Ne) and the immigration rate m (including nonreproductive individuals). Ne ranged between 4.1 and 19.3 individuals, Ne/N ranged between 0.05 and 0.65 and always decreased with N; m was estimated as 0.19-0.63, and was possibly biased upwards. We discuss how genotypic data can reveal fine-scale demographic processes with important microevolutionary implications.     

变温和恒温对沙葱萤叶甲发育速率的影响

沙葱萤叶甲为近年来在内蒙古草原猖獗成灾的新害虫,为明确温度对其发育速率的影响,分别设置5个变温组合(8/20℃,11/23℃,14/26℃,17/29℃和20/32℃)和6个恒温(13℃,17℃,21℃,25℃,29℃和33℃),比较了变温和恒温对沙葱萤叶甲幼虫和蛹发育速率的影响。结果表明,不同变温组合和恒温对沙葱萤叶甲幼虫和蛹的发育速率有显著的影响。发育历期随温度的升高而缩短,在变温条件下,1龄幼虫期、2龄幼虫期、3龄幼虫期、总幼虫期和蛹期分别从最低温度组合(8/20℃,平均15℃)的11.00,13.44,23.18,46.42和16.89 d,缩短至最高温度组合(20/32℃,平均27℃)的4.92,4.63,9.17,17.83和5.83 d;在恒温条件下,13℃下幼虫不能发育和存活,1龄幼虫期、2龄幼虫期、3龄幼虫期、总幼虫期和蛹期分别从17℃的14.50,10.75,20.63,45.50和11.00 d,缩短至33℃的6.10,5.47,10.60,22.17和5.33 d。在变温条件下,幼虫和蛹的发育起点温度分别为7.44℃和8.48℃,有效积温分别为344.82日度和113.52日度;在恒温条件下,幼虫和蛹的发育起点温度分别为0.64℃和5.11℃,有效积温分别为714.28日度和147.06日度。变温促进了沙葱萤叶甲幼虫和蛹的发育,本研究结果为沙葱萤叶甲的预测预报及综合防控提供了科学依据。     

A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Reduced representation genome sequencing such as restriction‐site‐associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome‐wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome‐wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long‐term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome.