花生MYB转录因子的鉴定与生物信息学分析

MYB转录因子是植物中重要的基因家族之一,参与多种生物学功能的调控.目前对花生(Arachis hypogaea)MYB转录因子家族的功能仍知之甚少,对花生中MYB转录因子的鉴定及生物信息学分析具有重要的意义.本研究在栽培花生中共鉴定出MYB转录因子443个,包括219个1R-MYB、209个2R-MYB、12个3R-...     

人类基因组中突变对紧邻碱基的依赖性与重组率

减数分裂重组通过基因转变、碱基替换等方式影响基因组进化。紧邻碱基对突变偏好性有很强的影响,但该“紧邻碱基效应”如何随重组率变化有待深入研究。本文提出基于条件互信息(Conditional mutual information)量化突变对紧邻碱基依赖性的方法,并利用人类SNP等相关数据,分析重组率如何影响突变对紧邻碱基的依赖性。结果表明:在全基因组水平上, SNP位点上的突变对紧邻碱基的依赖性(即平均条件互信息)随着重组率的增加而增加;具体而言,当SNPs两侧碱基为A/G、C/G或C/T时,随着重组率的增加突变偏向性增强,但两侧碱基为A/A或T/T时,重组率对SNP突变偏向性产生抑制作用;另外,重组率越高,外显子与基因间区SNP的突变偏好性越强;而内含子区域SNP的突变偏好受到高重组率的抑制。结果有助于深入理解减数分裂重组如何影响基因组进化。     

Recent Selection on Synonymous Codon Usage in Drosophila

Evidence from a variety of sources indicates that selection has influenced synonymous codon usage in Drosophila. It has generally been difficult, however, to distinguish selection that acted in the distant past from ongoing selection. However, under a neutral model, polymorphisms usually reflect more recent mutations than fixed differences between species and may, therefore, be useful for inferring recent selection. If the ancestral state is preferred, selection should shift the frequency distribution of derived states/site toward lower values; if the ancestral is unpreferred, selection should increase the number of derived states/site. Polymorphisms were classified as ancestrally preferred or unpreferred for several genes of D. simulans and D. melanogaster. A computer simulation of coalescence was employed to derive the expected frequency distributions of derived states/site under various modifications of the Wright–Fisher neutral model, and distributions of test statistics (t and Mann–Whitney U) were derived by appropriate sampling. One-tailed tests were applied to transformed frequency data to assess whether the two frequency distributions deviated from neutral expectations in the direction predicted by selection on codon usage. Several genes from D. simulans appear to be subject to recent selection on synonymous codons, including one gene with low codon bias, esterase-6. Selection may also be acting in D. melanogaster. Received: 15 April 1998 / Accepted: 13 May 1999     

Variably male-biased sex ratio in a marine bird with females larger than males

When the costs of rearing males and females differ progeny sex ratios are expected to be biased toward the less expensive sex. Blue-footed booby (Sula nebouxii) females are larger and roughly 32% heavier than males, thus presumably more costly to rear. We recorded hatching and fledging sex ratios in 1989, and fledging sex ratios during the next 5 years. In 1989, the sample of 751 chicks showed male bias at hatching (56%) and at fledging (57% at ˜90 days). Fledging sex ratios during the five subsequent reproductive seasons were at unity (1 year) or male-biased, varying from 56% to 70%. Male bias was greater during years when mean sea surface temperature was warmer and food was presumably in short supply. During two warm-water years (only) fledging sex ratio varied with hatching date. Proportions of male fledglings increased with date from 0.48 to 0.73 in 1994, and from 0.33 to 0.79 in 1995. Similar results were obtained when the analysis was repeated using only broods with no nestling mortality, suggesting that the overall increase in the proportion of males over the season was the result of sex ratio adjustments at hatching. The male-biased sex ratio, and the increased male bias during poor breeding conditions supports the idea that daughters may be more costly than sons, and that their relative cost increases in poor conditions. Received: 3 February 1998 / Accepted: 12 September 1998     

Bias in Butterfly Distribution Maps: The Effects of Sampling Effort

Data from the Greater Manchester Butterfly Atlas (UK) reveal a highly significant and substantial impact of visits on both species' richness and species' incidence in squares. This effect has been demonstrated for three different zones mapped at different scales. The significant impact of number of visits persists when data are amalgamated for coarser scales. The findings demonstrate that it is essential for distribution mapping projects to record data on recording effort as well as on the target organisms. Suggestions are made as to how distribution mapping may be improved, including a geographically and environmentally representative structure of permanently monitored squares and closer links between distribution mapping and the Butterfly Monitoring Scheme (BMS), which primarily monitors changes in butterfly populations. The benefit to conservation will be data that can be better used to analyse the reasons for changes in ranges and distributions, fundamental for determining priorities and policy decisions.     

Unbiased estimation of individual asymmetry

The importance of measurement error (ME) for the estimation of population level fluctuating asymmetry (FA) has long been recognized. At the individual level, however, this aspect has been studied in less detail. Recently, it has been shown that the random slopes of a mixed regression model can estimate individual asymmetry levels that are unbiased with respect to ME. Yet, recent studies have shown that such estimates may fail to reflect heterogeneity in these effects. In this note I show that this is not the case for the estimation of individual asymmetry. The random slopes adequately reflect between‐individual heterogeneity in the underlying developmental instability. Increased levels of ME resulted in, on average, lower estimates of individual asymmetry relative to the traditional unsigned asymmetry. This well‐known shrinkage effect in Bayesian analysis adequately corrected for ME and heterogeneity in ME resulting in unbiased estimates of individual asymmetry that were more closely correlated with the true underlying asymmetry.     

On the use of parataxonomy in biodiversity monitoring: a case study on wild flora

Monitoring programs that assess species-richness and turnover are now regarded as essential to document biodiversity loss worldwide. Implementation of such programs is impeded by a general decrease in the number of skilled naturalists. Here we studied how morphotypes, instead of species, might be used by unskilled participants (referred to as “volunteers”) to survey common plant communities. Our main questions were: (1) Can morphotypes be used as a robust estimator of species-richness (α-diversity) and assemblage turnover (β-diversity)? and (2) What is the robustness (reproducibility and repeatability) of such methods? Double inventories were performed on 150 plots in arable field margins, one by a non-expert using morphotypes, the other by a taxonomist using species. To test the robustness of morphotype identification among participants, 20 additional plots were surveyed by eight volunteers using the same protocol. We showed that (1) the number of morphotypes identified by unskilled volunteers in a plot was always strongly correlated with species-richness. (2) Morphotypes were sensitive to differences among habitats but were less accurate than species to detect these differences. (3) Morphotype identification varied significantly within and between volunteers. Due to this lack of repeatability and reproducibility, parataxonomy cannot be considered a good surrogate for taxonomy. Nevertheless, assuming that morphotypes are identified with standardized methods, and that results are used only to evaluate gross species-richness but not species turnover, parataxonomy might be a valuable tool for rapid biodiversity assessment of common wild flora.