Mechanisms and consequences of widespread random monoallelic expression

Although random monoallelic expression has been known for decades to affect genes on the X chromosome in female placental mammals, until a few years ago it was thought that there were few autosomal genes that were regulated in this manner. New tools for assaying gene expression genome-wide are now revealing that there are perhaps more genes that are subject to random monoallelic expression on mammalian autosomes than there are on the X chromosome and that these expression properties are achieved by diverse molecular mechanisms. This mode of expression has the potential to have an impact on natural selection and on the evolution of gene families.     

Costs of sexual traits: a mismatch between theoretical considerations and empirical evidence

Costs of sexual traits are of central importance to the theory of sexual selection. To qualify as a cost in line with theoretical models, empirical studies must demonstrate that sexual traits cause negative effects on one component of fitness of the trait bearer. Moreover, it must be demonstrated that the costs are differential such that negative effects on fitness are more severe for individuals in poor condition than for individuals in good condition. However, in the current literature, there is confusion over what qualifies as a cost, and costs are often anticipated based on findings of increased expenditure. Consequently, it seems that the generally accepted notion that sexual traits are costly is in fact based almost exclusively on indirect evidence and that direct empirical evidence is very scarce.     

几种植物组织及其原生质体过氧化物酶同工酶的比较研究

对马尾松幼苗子叶和胚轴、甘蔗、小麦、烟草、黄花菜等幼叶及其原生质体的过氧化物酶同工酶(POI)分别作比较研究。观察到凡经纤维素酶处理的各植物组织POI酶带数均多于未经纤维素酶处理的组织的酶带数;除个别例外,后者一般又比无壁原生质体的酶带数多。此种差异随植株生长年龄而增大,表明植物组织内大部分POI主要存于质外体中。     

Diversity of butterflies on British islands: ecological influences underlying the roles of area, isolation and the size of the faunal source

To distinguish between the influences of area and isolation on the butterfly faunas of British islands two approaches are adopted. First, species richness is related to island area, isolation and the size of the faunal source. Neither area nor isolation account for much variance in species richness, though area is more important than isolation. In contrast, species richness corresponds closely to the size of the faunal source on nearby islands and to that at proximate locations on adjacent mainlands. The second approach relates the incidence of species on islands to their ecological attributes. A very close relationship is found between species incidence on islands and those ecological variables that measure potential for migration and colonization and that resist extinction. The implications are that the majority of British islands in this survey are insufficiently isolated to prevent intermittent migrations of butterflies to them or so small as to generate frequent extinctions. Independent data indicate the capacity of many resident species to migrate distances in excess of the isolation of most of the islands. Some evidence also exists for the long-term survival of species on islands; important considerations in this respect are that most islands in the survey are large compared to habitat patches sustaining species on mainland Britain and that substantial portions of islands are retained in early seral stages or comprise long-lived stable habitats (e.g. peat mosses) that are particularly suitable for many British species.     

The organization of NADH dehydrogenase polypeptides in the inner mitochondrial membrane.

The organization of the constituent polypeptides of mitochondrial NADH dehydrogenase was studied by using two membrane-impermeable probes, diazobenzene[35S]sulphonate and lactoperoxidase-catalysed radioiodination. The incorporation of label into the subunits of the isolated enzyme was compared with that obtained with enzyme immunoprecipitated from labelled mitochondria or inverted submitochondrial particles. On the basis of accessibility to these two labels, we divide the polypeptides of Complex I into five groups: those that are apparently buried in the enzyme, those that are accessible to labelling in the isolated enzyme but not in the membrane, those that are exposed on the cytoplasmic face of the membrane, those that are exposed on the matrix face and finally those that are exposed on both faces and are therefore transmembranous. We conclude that NADH dehydrogenase is asymmetrically organized across the inner mitochondrial membrane.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Missense meanderings in sequence space: a biophysical view of protein evolution

Proteins are finicky molecules; they are barely stable and are prone to aggregate, but they must function in a crowded environment that is full of degradative enzymes bent on their destruction. It is no surprise that many common diseases are due to missense mutations that affect protein stability and aggregation. Here we review the literature on biophysics as it relates to molecular evolution, focusing on how protein stability and aggregation affect organismal fitness. We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution.     

基因型错误对数量性状精细定位的哈迪-温伯格不平衡指数的效应

使用紧密相邻的标记位点且与标记基因频率无关的哈迪-温伯格不平衡(HWD)指数被用来对数量性状位点(QTL)进行精细定位.本文讨论了当存在基因型错误时HWD指数的性质.文章指出,当存在基因型错误时,对于在群体的标记基因频率已知的情形使用的两个HWD指数尽管受基因型错误的影响但仍然有效;而仅仅极端样本的标记基因频率已知的情形下使用的两个HWD指数同时与基因型错误和标记基因频率有关.计算机模拟表明,仅仅极端样本的标记基因频率已知的情形下使用的两个HWD指数在精细定位时会产生偏差,不适宜作精细定位.     

Arbuscular mycorrhizal fungi affect phytophagous insect specialism

The majority of phytophagous insects eat very few plant species, yet the ecological and evolutionary forces that have driven such specialism are not entirely understood. The hypothesis that arbuscular mycorrhizal (AM) fungi can determine phytophagous insect specialism, through differential effects on insect growth, was tested using examples from the British flora. In the UK, plant families and species in the family Lamiaceae that are strongly mycorrhizal have higher proportions of specialist insects feeding on them than those that are weakly mycorrhizal. We suggest that AM fungi can affect the composition of insect assemblages on plants and are a hitherto unconsidered factor in the evolution of insect specialism.     

Robust indices of Hardy-Weinberg disequilibrium for QTL fine mapping

Hardy-Weinberg disequilibrium (HWD) measures have been proposed using dense markers to fine map a quantitative trait locus (QTL) to regions < approximately 1 cM. Earlier HWD measures may introduce bias in the fine mapping because they are dependent on marker allele frequencies across loci. Hence, HWD indices that do not depend on marker allele frequencies are desired for fine mapping. Based on our earlier work, here we present four new HWD indices that do not depend on marker allele frequencies. Two are for use when marker allele frequencies in a study population are known, and two are for use when marker allele frequencies in a study population are not known and are only known in the extreme samples. The new measures are a function of the genetic distance between the marker locus and a QTL. Through simulations, we investigated and compared the fine mapping performance of the new HWD measures with that of the earlier ones. Our results show that when marker allele frequencies vary across loci, the new measures presented here are more robust and powerful.     

Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins

Patterns in amino acid properties (polar, hydrophobic, etc.) that characterize secondary structure motifs are derived from a database containing 75 protein structures, with the aim of circumventing the limitations due to data base size so as to increase structure prediction score. Many such sequence-structure associations with high intrinsic predictive power are found, which turn out to be correct 78% of the time when applied individually to proteins outside the learning set. Based on these associations, a prediction method is developed, which reaches the score of 62% on the 3 states alpha-helix, beta-strand, and loop, without using additional constraints. Though this score is quite good compared to that of other available prediction methods, it is much lower than could be expected from the high intrinsic predictive power of the associations used. The reasons underlying this surprising result, which indicate that prediction score and intrinsic predictive power are only weakly coupled, are discussed. It is also shown that the size of the present database still seriously limits prediction scores, even when property patterns are used, and that higher scores are expected in large databases. Clues are provided on the relative influence of neglecting spatial interactions on prediction efficiency, suggesting that, in sufficiently large databases, predicted secondary structures would correspond to those formed early in the folding process. This hypothesis is tested by confronting present predictions with available experimental data on early protein folding intermediates and on small peptides that adopt a relatively stable conformation in water. Although admittedly there are still too few such data, results suggest that the hypothesis might be well founded.     

6种松科植物叶表皮的扫描电镜观察

应用扫描电子显微镜,观察了松科(Pinaceae)3个属6种植物叶表皮特征。金钱松气孔带位下表面,气孔区与非气孔区表皮细胞形态差异很大,气孔细缝状;雪松针叶四面都具气孔线,气孔下陷,孔口光滑,针叶表面具较厚的角质层,表皮细胞形状观察不清;五针松针叶仅两腹面有气孔线,气孔有隆起的圆环围绕,表面角质层呈条纹状排列,形成一种沟槽;黑松、湿地松、马尾松针叶腹背面都有气孔线,气孔呈蜂窝状排列成行,气孔下陷,孔口角质化强烈。结果表明松科3个属植物叶表皮的形态结构及气孔器差异显著,一定程度上证实了3属是自然的分类群。     

Gender features and interpretation: a case study

Are features on nouns associated with an interpretation? This is debated in the case of number, where some say that number features on nouns are interpreted, and others say that they are a mere reflex of an interpreted feature located elsewhere. This paper looks at gender features in Italian, where the gender a noun can have is not arbitrary, and it seeks to account for the restrictions that gender seems to impose on interpretation. It argues that gender features on Italian nouns are indeed associated with an interpretation. At the same time, however, there is a special process, subject to various conditions, that has the result that in certain contexts their contribution can be ignored. The paper thus defends a view on which interpretable elements can sometimes go uninterpreted. Gender features are among the elements that can do so.     

Multiple parthenoforms of Empoasca leafhoppers from Madeira Island: where are these unisexual forms coming from?

There are controversial opinions on whether asexual reproduction is more common on islands than on the mainland. Although some authors consider that the evidences of geographical parthenogenesis support the view that asexual reproduction is more common on islands, comparative data on the modes of reproduction of insular and continental taxa confirming this statement are very limited. In this work, we report the presence of three unisexual forms and three bisexual species of the genus Empoasca (Cicadelloidea, Hemiptera, Insecta) from Madeira Island. Experimentally, the unisexual forms reproduced in the absence of males for several generations. The chromosome analysis has shown that the bisexual species differ from one another in chromosome number, and unisexual forms are apomictic and also each have different chromosome numbers. Of parthenoforms, one is triploid and two are of obscure level of ploidy, 2n or 3n. The results obtained show that for this genus unisexual forms are more common on Madeira Island than in the nearby continental areas. It is suggested that unisexual forms may be more plentiful on islands than on the mainland because if an asexual reproduction event occurs, the relaxing competition in these underexploited and enemy-free habitats may favor the establishment of new parthenogenetic lineages.     

浙江海岛鸟兽地理生态学的初步研究

对浙江洞头岛及舟山五岛的鸟兽调查表明,海岛动物的种数较相邻大陆为低,但种群密度却高于大陆,岛上的某些种类出现生态位扩展的现象。舟山五岛兽类的种数和岛屿面积呈正相关,其关系式为S=2.12A~(0.29),但种群密度随着岛屿面积的增大而下降。文中据此提出了保护和发展岛屿动物资源的某些措施。     

Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell

Stromules are motile extensions of the plastid envelope membrane, whose roles are not fully understood. They are present on all plastid types but are more common and extensive on non-green plastids that are sparsely distributed within the cell. During tomato fruit ripening, chloroplasts in the mesocarp tissue differentiate into chromoplasts and undergo major shifts in morphology. In order to understand what factors regulate stromule formation, we analysed stromule biogenesis in tobacco hypocotyls and in two distinct plastid populations in tomato mesocarp. We show that increases in stromule length and frequency are correlated with chromoplast differentiation, but only in one plastid population where the plastids are larger and less numerous. We used tobacco hypocotyls to confirm that stromule length increases as plastids become further apart, suggesting that stromules optimize the plastid-cytoplasm contact area. Furthermore, we demonstrate that ectopic chloroplast components decrease stromule formation on tomato fruit chromoplasts, whereas preventing chloroplast development leads to increased numbers of stromules. Inhibition of fruit ripening has a dramatic impact on plastid and stromule morphology, underlining that plastid differentiation status, and not cell type, is a significant factor in determining the extent of plastid stromules. By modifying the plastid surface area, we propose that stromules enhance the specific metabolic activities of plastids.     

On the use of the Price equation

This paper distinguishes two categories of questions that the Price equation can help us answer. The two different types of questions require two different disciplines that are related, but nonetheless move in opposite directions. These disciplines are probability theory on the one hand and statistical inference on the other. In the literature on the Price equation this distinction is not made. As a result of this, questions that require a probability model are regularly approached with statistical tools. In this paper, we examine the possibilities of the Price equation for answering questions of either type. By spending extra attention on mathematical formalities, we avoid the two disciplines to get mixed up. After that, we look at some examples, both from kin selection and from group selection, that show how the inappropriate use of statistical terminology can put us on the wrong track. Statements that are 'derived' with the help of the Price equation are, therefore, in many cases not the answers they seem to be. Going through the derivations in reverse can, however, be helpful as a guide how to build proper (probabilistic) models that do give answers.     

Profile-based direct kernels for remote homology detection and fold recognition

MOTIVATION: Protein remote homology detection is a central problem in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for remote homology detection. The performance of these methods depends on how the protein sequences are modeled and on the method used to compute the kernel function between them. RESULTS: We introduce two classes of kernel functions that are constructed by combining sequence profiles with new and existing approaches for determining the similarity between pairs of protein sequences. These kernels are constructed directly from these explicit protein similarity measures and employ effective profile-to-profile scoring schemes for measuring the similarity between pairs of proteins. Experiments with remote homology detection and fold recognition problems show that these kernels are capable of producing results that are substantially better than those produced by all of the existing state-of-the-art SVM-based methods. In addition, the experiments show that these kernels, even when used in the absence of profiles, produce results that are better than those produced by existing non-profile-based schemes. AVAILABILITY: The programs for computing the various kernel functions are available on request from the authors.     

spalt-induced specification of distinct dorsal and ventral domains is required for Drosophila tracheal patterning

Morphogenesis of the Drosophila tracheal system relies on different signalling pathways that have distinct roles in specifying both the migration of the tracheal cells and the particular morphological features of the primary branches. The current view is that the tracheal cells are initially specified as an equivalent group of cells whose diversification depends on signals from the surrounding cells. In this work, we show that the tracheal primordia are already specified as distinct dorsal and ventral cell populations. This subdivision depends on the activity of the spalt (sal) gene and occurs prior to the activity of the signalling pathways that dictate the development of the primary branches. Finally, we show that the specification of these two distinct cell populations, which are not defined by cell lineage, are critical for proper tracheal patterning. These results indicate that tracheal patterning depends not only on signalling from surrounding cells but also in the different response of the tracheal cells depending on their allocation to the dorsal or ventral domains.     

Morphological Adaptation of Inflorescences in Plants that Develop at Low Temperatures in Early Spring: The Convergent Evolution of "Downy Plants"

Abstract: A new category of plants that exhibit convergent evolution, namely "downy plants", is described and discussed here on the bais of natural selection. So-called snowball plants can be represented by Saussurea gossypiphora D. Don (Compositae), which has extremely dense trichomes on well-developed bracts that are tightly packed around floral buds. Plants whose morphology is similar to that of S. gossypiphora are found at high elevations of alpine zones in the Nepalese Himalayas, where temperatures are low and precipitation is high (frequent rain) in summer. Nonetheless, we noticed that plants with a morphology similar to that of Himalaya snowball plants are commonly distributed from temperature to Arctic zones, and are even found in Alaska where precipitation is very limited. Willows ( Salix spp.: Salicaceae) and deciduous magnolias (Magnoliaceae) are typical examples of such plants. Measurements of temperature inside and outside the inflorescences of Salix (pussy willow or catkin) and of Magnolia suggested that the pubescent bracts might play a role in keeping the interior of buds warm, but that the effect depends on light intensity. Our examination of such species led us to extend the concept of "snowball plants" to a larger group of plants, namely "downy plants", that are characterized by very dense trichomes on tightly packed bracts of inflorescences. Downy plants are thereby considered to represent a convergent adaptation that allows blooming at low temperatures.