Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny

The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods examined were the neighbor joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and both nucleotide sequences and deduced amino acid sequences were analyzed. Generally speaking, amino acid sequences were better than nucleotide sequences in obtaining the true tree (topology) or trees close to the true tree. However, when only first and second codon positions data were used, nucleotide sequences produced reasonably good trees. Among the 13 genes examined, Nd5 produced the true tree in all tree-building methods or algorithms for both amino acid and nucleotide sequence data. Genes Cytb and Nd4 also produced the correct tree in most tree-building algorithms when amino acid sequence data were used. By contrast, Co2, Nd1, and Nd41 showed a poor performance. In general, large genes produced better results, and when the entire set of genes was used, all tree-building methods generated the true tree. In each tree-building method, several distance measures or algorithms were used, but all these distance measures or algorithms produced essentially the same results. The ME method, in which many different topologies are examined, was no better than the NJ method, which generates a single final tree. Similarly, an ML method, in which many topologies are examined, was no better than the ML star decomposition algorithm that generates a single final tree. In ML the best substitution model chosen by using the Akaike information criterion produced no better results than simpler substitution models. These results question the utility of the currently used optimization principles in phylogenetic construction. Relatively simple methods such as the NJ and ML star decomposition algorithms seem to produce as good results as those obtained by more sophisticated methods. The efficiencies of the NJ, ME, MP, and ML methods in obtaining the correct tree were nearly the same when amino acid sequence data were used. The most important factor in constructing reliable phylogenetic trees seems to be the number of amino acids or nucleotides used.      

Quantitative trait loci with age-specific effects on fecundity in Drosophila melanogaster

Life-history theory and evolutionary theories of aging assume the existence of alleles with age-specific effects on fitness. While various studies have documented age-related changes in the genetic contribution to variation in fitness components, we know very little about the underlying genetic architecture of such changes. We used a set of recombinant inbred lines to map and characterize the effects of quantitative trait loci (QTL) affecting fecundity of Drosophila melanogaster females at 1 and 4 weeks of age. We identified one QTL on the second chromosome and one or two QTL affecting fecundity on the third chromosome, but these QTL affected fecundity only at 1 week of age. There was more genetic variation for fecundity at 4 weeks of age than at 1 week of age and there was no genetic correlation between early and late-age fecundity. These results suggest that different loci contribute to the variation in fecundity as the organism ages. Our data provide support for the mutation accumulation theory of aging as applied to reproductive senescence. Comparing the results from this study with our previous work on life-span QTL, we also find evidence that antagonistic pleiotropy may contribute to the genetic basis of senescence in these lines as well.     

胸内正压对正常人左室功能影响及其力学原理

目的：探讨胸内正压对正常人左室射血及充盈的影响及其力学原理。方法：超声心动图观测30例正常人初始时与标准乏氏动作张力期10s时左室舒张末容积（LVEDV）、左室收缩末容积（LVESV）、每搏量（SV）、射血分值（EF）、流入道血流速度（E峰、A峰）、E／A值、二尖瓣环舒张早期运动速度（e）及舒张早期充盈压（E/e）的变化。结果：与初始时比较,标准乏氏动作张力期LVEDV、LVESV及SV减低而心率（陬）增快（P均〈0．001）,EF值增加,但无统计学意义（P〉0．05）;E峰与E／A值减低（P均〈O．05）;e没有变化（P〉0．05）．E／e值减低（P〈O．05）。结论：胸内正压对左室游离壁的力学作用促进了左室收缩运动而阻碍了左室舒张运动,会引起EF值增加,E峰及E／A值减低;2,胸内正压降低了肺静脉系统与心脏的跨壁压力,增加了血流阻力也是导致肺静脉系统与左室血液回流减少．E峰减低．E／e值减低的一个原因。     

Dynamics of genetic adaptation to captivity

Many species require captive breeding to savethem from extinction, with reintroduction intothe wild being the eventual aim of mostprograms. Adaptation to captive environmentstypically results in reduced fitness under wildconditions. Consequently, unintentionaladaptation during captive breeding programs mayseriously compromise the success ofreintroduction programs. However, there islittle experimental evidence on the rate orextent of adaptation for captive populationsmaintained under benign captive conditions forextended periods of time. To investigate thedynamics of genetic adaptation to captivity,large captive populations of Drosophilamelanogaster were assessed for relativefitness under captive conditions for up to 87generations in captivity. Captive fitnessincreased to 3.33 times the initial fitnessover 87 generations. The pattern of adaptationwas curvilinear, with an exponential curveproviding the best fit. Fitness reached 25% ofits maximum within 6 generations, 50% within15 generations, 75% within 31 generations and95% within 67 generations. The model predictedthat the asymptotic level of fitness reachedwould be 3.38 times the initial fitness. Thus,very large genetic adaptations to captivity mayoccur under relatively benign captiveconditions. Captive populations destined forreintroduction need to be managed to minimisegenetic adaptation to captivity.     

Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics

Only relatively recently have researchers turned to molecular methods for nematode phylogeny reconstruction. Thus, we lack the extensive literature on evolutionary patterns and phylogenetic usefulness of different DNA regions for nematodes that exists for other taxa. Here, we examine the usefulness of mtDNA for nematode phylogeny reconstruction and provide data that can be used for a priori character weighting or for parameter specification in models of sequence evolution. We estimated the substitution pattern for the mitochondrial ND4 gene from intraspecific comparisons in four species of parasitic nematodes from the family Trichostrongylidae (38-50 sequences per species). The resulting pattern suggests a strong mutational bias toward A and T, and a lower transition/transversion ratio than is typically observed in other taxa. We also present information on the relative rates of substitution at first, second, and third codon positions and on relative rates of saturation of different types of substitutions in comparisons ranging from intraspecific to interordinal. Silent sites saturate extremely quickly, presumably owing to the substitution bias and, perhaps, to an accelerated mutation rate. Results emphasize the importance of using only the most closely related sequences in order to infer patterns of substitution accurately for nematodes or for other taxa having strongly composition-biased DNA. ND4 also shows high amino acid polymorphism at both the intra- and interspecific levels, and in higher level comparisons, there is evidence of saturation at variable amino acid sites. In general, we recommend using mtDNA coding genes only for phylogenetics of relatively closely related nematode species and, even then, using only nonsynonymous substitutions and the more conserved mitochondrial genes (e.g., cytochrome oxidases). On the other hand, the high substitution rate in genes such as ND4 should make them excellent for population genetics studies, identifying cryptic species, and resolving relationships among closely related congeners when other markers show insufficient variation.      

变性高效液相色谱技术对创伤弧菌检测的研究

应用PCR结合变性高效液相色谱技术对创伤弧菌进行检测,建立创伤弧菌快速准确的检测新方法。经过DHPLC分析条件优化,在DHPLC非变性温度下分析创伤弧菌特异性PCR扩增产物。同时进行方法特异性、灵敏度、重复性实验。实验结果表明所建立的创伤弧菌PCR-DHPLC检测方法特异性强、灵敏度高、重现性好、结果稳定可靠、检测时间短,检测低限可达到124 CFU/mL,是创伤弧菌快速检测的新技术。     

Invasion and persistence of plant parasites in a spatially structured host population

Spatial structure is of central importance in the dynamics of plant-parasite interactions and is imposed by the growth habit and distribution of host plants and by parasite dispersal which is frequently restricted. To investigate the effects of spatial heterogeneity on the dynamics of plant parasites we introduce a simple model for epidemic development within a spatially structured host population. Here the host population is subdivided into a number of patches which are linked to allow for transmission from one patch to another with the connections defining the spatial structure of the host population. Three key parameters are identified that play a critical role in the ability of the parasite to invade and persist within the host population: the within-patch parasite basic reproductive number which characterises the infection dynamics at the local spatial scale; and the neighbourhood of interaction which describes which patches interact with which and the strength of coupling between patches within the neighbourhood which together characterise the spread of the parasite over larger spatial scales. Using both deterministic and stochastic formulations of the model, we investigate how the thresholds and probabilities of invasion and persistence are affected by these parameters, by demographic stochasticity and by differences in the initial level of infection.     

Comparative losses of quantitative and molecular genetic variation in finite populations of Drosophila melanogaster

Quantitative genetic variation, the main determinant of the ability to evolve, is expected to be lost in small populations, but there are limited data on the effect, and controversy as to whether it is similar to that for near neutral molecular variation. Genetic variation for abdominal and sternopleural bristle numbers and allozyme heterozygosity were estimated in 23 populations of Drosophila melanogaster maintained at effective population sizes of 25, 50, 100, 250 or 500 for 50 generations, as well as in 19 highly inbred populations and the wild outbred base population. Highly significant negative regressions of proportion of initial genetic variation retained on inbreeding due to finite population size were observed for both quantitative characters (b = -0.67 +/- 0.14 and -0.58 +/- 0.11) and allozyme heterozygosity (b = -0.79 +/- 0.10), and the regression coefficients did not differ significantly. Thus, quantitative genetic variation is being lost at a similar rate to molecular genetic variation. However, genetic variation for all traits was lost at rates significantly slower than predicted by neutral theory, most likely due to associative overdominance. Positive, but relatively low correlations were found among the different measures of genetic variation, but their low magnitudes were attributed to large sampling errors, rather than differences in the underlying processes of loss.     

Resource allocation for epidemic control in metapopulations

Deployment of limited resources is an issue of major importance for decision-making in crisis events. This is especially true for large-scale outbreaks of infectious diseases. Little is known when it comes to identifying the most efficient way of deploying scarce resources for control when disease outbreaks occur in different but interconnected regions. The policy maker is frequently faced with the challenge of optimizing efficiency (e.g. minimizing the burden of infection) while accounting for social equity (e.g. equal opportunity for infected individuals to access treatment). For a large range of diseases described by a simple SIRS model, we consider strategies that should be used to minimize the discounted number of infected individuals during the course of an epidemic. We show that when faced with the dilemma of choosing between socially equitable and purely efficient strategies, the choice of the control strategy should be informed by key measurable epidemiological factors such as the basic reproductive number and the efficiency of the treatment measure. Our model provides new insights for policy makers in the optimal deployment of limited resources for control in the event of epidemic outbreaks at the landscape scale.