Modeling the distribution of a wide‐ranging invasive species using the sampling efforts of expert and citizen scientists

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Spatial association of genetically similar Atlantic salmon juveniles and sex bias in spatial patterns in a river

Atlantic salmon ( Salmo salar ) juveniles were electrofished along a 300-m stretch of a river to test for possible associations between genetic similarity and geographical distance between individuals. Multilocus DNA fingerprinting showed that genetically similar juveniles (1–4 years old) were found closer together in the river than less related individuals. However, the association between genetic similarity and geographical distance, although significant, was not strong. This may indicate that factors other than genetic relatedness influence the positioning in the river. A sex bias in the relationship between genetic similarity and geographical distance was caused by a difference between sexually mature and immature males. The study shows that sampling of salmon juveniles should be spread over a wide stretch of the river in order to avoid sampling relatives. Moreover, by including several year classes, the overall degree of genetic similarity is effectively reduced compared with sampling individuals of similar age.     

Two Aspects of DNA Base Composition: G+C Content and Translation-Coupled Deviation from Intra-Strand Rule of A=T and G=C

The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A=T and G=C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint. Received: 5 November 1998 / Accepted: 1 March 1999     

Optimizing noninvasive sampling of a zoonotic bat virus

Outbreaks of infectious viruses resulting from spillover events from bats have brought much attention to bat‐borne zoonoses, which has motivated increased ecological and epidemiological studies on bat populations. Field sampling methods often collect pooled samples of bat excreta from plastic sheets placed under‐roosts. However, positive bias is introduced because multiple individuals may contribute to pooled samples, making studies of viral dynamics difficult. Here, we explore the general issue of bias in spatial sample pooling using Hendra virus in Australian bats as a case study. We assessed the accuracy of different under‐roost sampling designs using generalized additive models and field data from individually captured bats and pooled urine samples. We then used theoretical simulation models of bat density and under‐roost sampling to understand the mechanistic drivers of bias. The most commonly used sampling design estimated viral prevalence 3.2 times higher than individual‐level data, with positive bias 5–7 times higher than other designs due to spatial autocorrelation among sampling sheets and clustering of bats in roosts. Simulation results indicate using a stratified random design to collect 30–40 pooled urine samples from 80 to 100 sheets, each with an area of 0.75–1 m², and would allow estimation of true prevalence with minimum sampling bias and false negatives. These results show that widely used under‐roost sampling techniques are highly sensitive to viral presence, but lack specificity, providing limited information regarding viral dynamics. Improved estimation of true prevalence can be attained with minor changes to existing designs such as reducing sheet size, increasing sheet number, and spreading sheets out within the roost area. Our findings provide insight into how spatial sample pooling is vulnerable to bias for a wide range of systems in disease ecology, where optimal sampling design is influenced by pathogen prevalence, host population density, and patterns of aggregation.     

An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Phylogenetic codon models are routinely used to characterize selective regimes in coding sequences. Their parametric design, however, is still a matter of debate, in particular concerning the question of how to account for differing nucleotide frequencies and substitution rates. This problem relates to the fact that nucleotide composition in protein-coding sequences is the result of the interactions between mutation and selection. In particular, because of the structure of the genetic code, the nucleotide composition differs between the three coding positions, with the third position showing a more extreme composition. Yet, phylogenetic codon models do not correctly capture this phenomenon and instead predict that the nucleotide composition should be the same for all three positions. Alternatively, some models allow for different nucleotide rates at the three positions, an approach conflating the effects of mutation and selection on nucleotide composition. In practice, it results in inaccurate estimation of the strength of selection. Conceptually, the problem comes from the fact that phylogenetic codon models do not correctly capture the fixation bias acting against the mutational pressure at the mutation–selection equilibrium. To address this problem and to more accurately identify mutation rates and selection strength, we present an improved codon modeling approach where the fixation rate is not seen as a scalar, but as a tensor. This approach gives an accurate representation of how mutation and selection oppose each other at equilibrium and yields a reliable estimate of the mutational process, while disentangling the mean fixation probabilities prevailing in different mutational directions.     

New challenges in the study of the evolution of wild animals and their gut microbiome

In this viewpoint, by reviewing the recent findings on wild animals and their gut microbiomes, we found some potential new insights and challenges in the study of the evolution of wild animals and their gut microbiome. We suggested that wild animal gut microbiomes may come from microbiomes in the animals'' living habitats along with animals'' special behavior, and that the study of long‐term changes in gut microbiomes should consider both habitat and special behaviors. Also, host behavior would facilitate the gut microbiome transmission between individuals. We suggested that research should integrate the evolutionary history and physiological systems of wild animals to understand the evolution of animals and their gut microbiomes. Finally, we proposed the Noncultured‐Cultured‐Fermentation‐Model Animal pipeline to determine the function (diet digestion, physiology, and behavior) of these target strains in the wild animal gut.     

人骨形态发生蛋白7（hBMP7）在毕赤酵母中的分泌表达

依据酵母密码子使用偏好性,利用重叠延伸PCR(OE-PCR)介导的定点突变方法,对人骨形态发生蛋白-7(human Bone Morphogenetic Protein-7,hBMP7)成熟肽编码序列进行改造,将毕赤酵母低频使用的精氨酸密码子CGG或CGA突变为高频使用的同义密码子AGA,明显提高了hBMP7成熟肽在毕赤酵母中的表达量摇瓶培养表达量为25.45mg/L,是改造前序列的4.6倍;TricineSDS-PAGE及Western-blotting结果表明,rhBMP7成熟肽分子量为18kD,以单体形式存在,具有良好的免疫原性;利用梯度浓度G418筛选到一株高拷贝整合的转化子,该转化子摇瓶表达量为45.45mg/L,约为单拷贝转化子的2倍。表达上清经阳离子交换介质SPSepharoseR○FastFlow纯化后,目的蛋白纯度达到90%。纯化后的样品与I型胶原混合冻干后埋植于小鼠股部肌袋内,能异位诱导间充质细胞分化形成软骨细胞。     

茶树CBF1基因密码子使用特性分析

转录因子CBF(C-repeat-binding factor)广泛存在于各种植物中, 是植物抗逆过程中一个重要的调节因子。文章运用CHIPS、CUSP和CodonW在线程序对茶树(Camellia sinensis)CBF1基因(CsCBF1)序列进行分析, 并与茶树基因、模式植物基因组和其他植物CBF基因进行比较, 对了解CsCBF1基因密码子使用特性, 并为其选择合适的表达系统具有重要意义。结果表明：CsCBF1基因与70个茶树基因对密码子的使用有明显的差异, CsCBF1基因偏好使用以G/C结尾的密码子, 而筛选的70个茶树基因偏好使用以A/T结尾的密码子。在密码子使用频率上, CsCBF1基因与拟南芥(Arabidopsis thaliana)、烟草(Nicotiana tobacum)的差异小于与小麦(Triticum aestivum)、玉米(Zea mays)的差异; 因此, 拟南芥、烟草更适合作为CsCBF1基因的外源表达宿主。通过分析40种植物CBF基因编码特点可知大部分CBF基因偏好使用以G/C结尾的密码子, 这可能与基因的特殊功能有关。     

Mutational equilibrium model of genome size evolution

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories). Instead the genome size is suggested to evolve until the loss of DNA through more frequent small deletions is equal to the rate of DNA gain through more frequent long insertions. The empirical basis for this theory is the finding of a strong correlation and of a clear power-function relationship between the rate of mutational DNA loss (per bp) through small deletions and genome size in animals. Genome size scales as a negative 1.3 power function of the deletion rate per nucleotide. Such a relationship is not predicted by either adaptive or junk DNA theories. However, if genome size is maintained at equilibrium by the balance of mutational forces, this empirilical relationship can be readily accommodated. Within this framework, this finding would imply that the rate of DNA gain through large insertions scales up a quarter-power function of genome size. On this view, as genome size grows, the rate of growth through large insertions is increasing as a quarter power function of genome size and the rate of DNA loss through small deletions increases linearly, until eventually, at the stable equilibrium genome size value, rates of growth and loss equal each other. The current data also suggest that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions. Both the origin of mutational biases and the adaptive consequences of such a mode of evolution of genome size are discussed.