Systematic analysis of genomic organization and heterogeneities of miRNA cluster in vertebrates

The clustering propensity of microRNA genes is a common biological phenomenon in various animal and plant species. To gain novel insight into genomic organization and potential functional heterogeneities of miRNA clusters in vertebrates from a genome scale, we used large scale data and presented a comprehensive analysis to examine various features of genomic organization of miRNA clusters across seven vertebrates by a combination of comparative genomics and bioinformatics approaches. The results of pair-wise distance analysis of same-strand consecutive miRNAs suggested that the fractions of the miRNA gene pairs are higher at relatively short pair-wise distances than those of protein-coding genes and other non-coding RNA genes. Especially relatively small number of miRNAs is more clustered at very short pair-wise distances than expected at random. We further observed significant difference between real miRNA clusters and randomly organized clusters for different aspects, including higher overlap of target genes, fewer seed types and significant enrichment in diseases. However, the extent of these features of clustered miRNAs has a different tendency and largely depends on inter-miRNA distances because of diverse clustering propensity of miRNAs in vertebrates, suggesting that this cooperated function or cooperative effects between miRNAs in clusters perhaps be affected by inter-miRNA distances.     

Using networks to analyze and visualize the distribution of overlapping genes in virus genomes

Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated open reading frames (ORFs) in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. Antisense overlaps in which one of the ORFs was encoded in the same frame on the opposite strand (−0) tend to be longer. Next, we develop a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family. In the absence of an unambiguous partition of ORFs by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent ORFs are adjacent in one or more genomes, and (2) that these ORFs overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.     

Comparative gene mapping in Arabidopsis lyrata chromosomes 1 and 2 and the corresponding A. thaliana chromosome 1: recombination rates, rearrangements and centromere location

To add detail to the genetic map of Arabidopsis lyrata, and compare it with that of A. thaliana, we have developed many additional markers in the A. lyrata linkage groups, LG1 and LG2, corresponding to A. thaliana chromosome 1. We used a newly developed method for marker development for single nucleotide polymorphisms present in gene sequences, plus length differences, to map genes in an A. lyrata family, including variants in several genes close to the A. thaliana centromere 1, providing the first data on the location of an A. lyrata centromere; we discuss the implications for the evolution of chromosome 1 of A. thaliana. With our larger marker density, large rearrangements between the two Arabidopsis species are excluded, except for a large inversion on LG2. This was previously known in Capsella; its presence in A. lyrata suggests that, like most other rearrangements, it probably arose in the A. thaliana lineage. Knowing that marker orders are similar, we can now compare homologous, non-rearranged map distances to test the prediction of more frequent crossing-over in the more inbreeding species. Our results support the previous conclusion of similar distances in the two species for A. lyrata LG1 markers. For LG2 markers, the distances were consistently, but non-significantly, larger in A. lyrata. Given the two species' large DNA content difference, the similarity of map lengths, particularly for LG1, suggests that crossing-over is more frequent across comparable physical distances in the inbreeder, A. thaliana, as predicted.     

Seasonal climatic niches diverge in migratory birds

Migratory birds occupy different geographical areas during breeding and non-breeding periods, and thus different factors may determine their range limits depending on each season. One such factor is the spatial climatic component of the niche, which is widely used to model species distributions, yet the temporal component is often neglected and is generally assumed to be constant. We tested the hypothesis that the climatic niche is conserved between breeding and non-breeding areas in 355 bird species migrating through Eurasian–African flyways. For this, we performed niche overlap analyses and compared niche differences between sister or phylogenetically closely related species, as well as linking the differences to migratory distances. For more than 80% of the species, there was no or very little overlap between their breeding and non-breeding climatic niches. For most closely related species, the degree of overlap of their breeding climatic niches was larger than the overlap observed within each species, but not for their wintering climatic niches, suggesting a phylogenetic conservation of breeding climatic niches. Finally, there was a clear negative relationship between migratory distances and climatic niche overlap within each species. Our results confirmed that the climatic niche of most Eurasian–African migratory species differs between both breeding and non-breeding ranges, suggesting distinctive seasonal climatic requirements. Given these results and the geographically uneven effects of climate change, the impact of global change is likely to have different effects in each seasonal range. Hence, both breeding and non-breeding climatic data need to be considered when using species distribution models.     

Plankton motility patterns and encounter rates

Many planktonic organisms have motility patterns with correlation run lengths (distances traversed before direction changes) of the same order as their reaction distances regarding prey, mates and predators (distances at which these organisms are remotely detected). At these scales, the relative measure of run length to reaction distance determines whether the underlying encounter is ballistic or diffusive. Since ballistic interactions are intrinsically more efficient than diffusive, we predict that organisms will display motility with long correlation run lengths compared to their reaction distances to their prey, but short compared to the reaction distances of their predators. We show motility data for planktonic organisms ranging from bacteria to copepods that support this prediction. We also present simple ballistic and diffusive motility models for estimating encounter rates, which lead to radically different predictions, and we present a simple criterion to determine which model is the more appropriate in a given case.     

Seabird metapopulations: searching for alternative breeding habitats

Today, many seabird species nest in port areas, which are also necessary for human economic activity. In this paper, we evaluate, using a metapopulation model, the possibilities for creating alternative breeding sites for the Common Tern (Sterna hirundo) in the Rhine–Meuse–Scheldt estuary. We explore 22 scenarios that differ with respect to (1) loss of breeding habitat in port areas, (2) location and size of newly created habitat, and (3) coexistence of old and new habitat. Results indicate that loss of port area habitats results in a serious 41% decline in the breeding population. When the loss in ports is compensated for within the ports, the decline was negligible. Fourteen scenarios result in an increase of the Common Tern metapopulation. In these, extra breeding habitat is created outside the ports in fish-rich waters, resulting in a potential metapopulation increase of 25%. However, the period of overlap between lost and newly created habitat strongly affects the results. A gap between the removal of old and the creation of new breeding areas might cause a drop in the metapopulation level of 30%. The population recovery from this drop might take more than 100 years due to slow recolonization. Our results suggest that conservation of seabird species should be evaluated on a metapopulation scale and that the creation of new habitat may help to compensate for habitat loss in other areas. Furthermore, the results indicate that overlap between the existence of old and newly created breeding habitats is crucial for the success of compensation efforts. However, new locations should be carefully selected, because not only is the suitability of the breeding grounds important, but ample fish availability nearby is also key. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Morphology and coexistence of congeneric ectoparasite species: reinforcement of reproductive isolation?

Assuming that differences or similarities in morphology among congeneric parasite species living in the same habitat are not a random pattern, several hypotheses explaining morphological differences were tested: (i) reproductive isolation, (ii) niche restriction resulting from competition, and (iii) niche specialization. Congeneric monogenean (platyhelminth) ectoparasites parasitizing the gills of one host species were used as an ecological model. Morphometric distances of the attachment organ and morphometric distances of the copulatory organ between species pairs were calculated, Levin's niche size and Renkonen niche overlap indices were applied. Our results support the prediction that the function of niche segregation is to achieve reproductive isolation of related species in order to prevent hybridization (reinforcement of reproductive barriers). Parasite species living in the same niche differ greatly in the size of copulatory organ. Moreover, species coexistence is facilitated by an increase in morphometric distances of copulatory organ and niche centre distances. Our results also show that species living in overlapping niches have similar attachment organs, which supports the prediction that morphologically similar species have the same ecological requirements within one host and suggests small effects of interspecific competition for the evolution of morphological diversity of attachment organs. Specialist adaptations also seem to facilitate species coexistence and affect the niche distribution within host species. Parasite species that can colonize more than one host species, i.e. generalists, occupy more distant niches within host species than strictly host-specific parasites. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76, 125–135.     

Expanding the subproteome of the inner mitochondria using protein separation technologies: one- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis

Currently no single proteomics technology has sufficient analytical power to allow for the detection of an entire proteome of an organelle, cell, or tissue. One approach that can be used to expand proteome coverage is the use of multiple separation technologies especially if there is minimal overlap in the proteins observed by the different methods. Using the inner mitochondrial membrane subproteome as a model proteome, we compared for the first time the ability of three protein separation methods (two-dimensional liquid chromatography using the ProteomeLab PF 2D Protein Fractionation System from Beckman Coulter, one-dimensional reversed phase high performance liquid chromatography, and two-dimensional gel electrophoresis) to determine the relative overlap in protein separation for these technologies. Data from these different methods indicated that a strikingly low number of proteins overlapped with less than 24% of proteins common between any two technologies and only 7% common among all three methods. Utilizing the three technologies allowed the creation of a composite database totaling 348 non-redundant proteins. 82% of these proteins had not been observed previously in proteomics studies of this subproteome, whereas 44% had not been identified in proteomics studies of intact mitochondria. Each protein separation method was found to successfully resolve a unique subset of proteins with the liquid chromatography methods being more suited for the analysis of transmembrane domain proteins and novel protein discovery. We also demonstrated that both the one- and two-dimensional LC allowed for the separation of the alpha-subunit of F1F0 ATP synthase that differed due to a change in pI or hydrophobicity.     

A chromosome-based model for estimating the number of conserved segments between pairs of species from comparative genetic maps

Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.     

浙江江山公益林物种种间关系及CCA排序

利用浙江省江山市80个公益林固定小班监测数据,基于生态位理论、种间联结、CCA排序方法对研究区内群落优势种种间关系及其与环境的关系进行研究。结果表明:江山市公益林群落中杉木、檵木、紫萁分别在乔木、灌木、草本层中占优势地位;石栎与青冈、隔药柃与山苍子、蕨与海金沙的生态位重叠指数值分别在乔、灌、草本层中最大;而CCA协变量矩阵偏典范对应分析说明物种分布主要受海拔、坡度、坡向(光照强度)以及腐殖质厚度的影响,总体上可以对89.44%的环境因子进行解释。并且还表明,生态位宽度较大的物种其生态位重叠值较大,并在CCA排序图物种集中区分布。反之,生态位重叠较小,在CCA排序图中将偏离物种集中区;除此之外,在CCA排序图上,物种间的距离与其生态位重叠值的大小及种间联结均有密切的关联,若未存在显著的联结性,随物种间的生态位重叠值越高,其在CCA排序上的距离越近,若存在显著联结性,则正相关缩小距离,负相关拉大距离。     

Evolutionary history and precipitation seasonality shape niche overlap in Neotropical bat–plant pollination networks

Species interactions are one dimension of a niche. Niche overlap arises when two species share an interaction partner. In pollination systems, environmental and biotic factors affect niche overlap. Here, we explored the effects of climate seasonality, plant and bat richness, morphological traits, and phylogenetic distance in shaping the niche overlap of Neotropical bat–plant pollination networks. We examined a dataset of 22 bat–plant pollination networks in the Neotropical region. We measured niche overlap in bats and plants with the Morisita-Horn index (Ĉ_H) and used a SAR model to test the relationships between niche overlap and both abiotic and biotic factors. We found a lower niche overlap among bats in communities composed of phylogenetically distant bat species. Moreover, plant and bat overlap was lower in regions with higher precipitation seasonality. Our results indicate that climate seasonality and bat evolutionary history drive niche overlap in Neotropical bat–plant pollination interactions. These findings suggest that a higher precipitation seasonality promotes the emergence of temporal modules, which reduces niche overlap, likely due to seasonal species phenologies. Furthermore, the method used to record the interactions affects the degree of niche overlap. Interactions recorded with pollen samples tend to have higher niche overlap than direct observations. The responses of morphological traits and phylogenetic distances in bat niche overlap were uncoupled, suggesting an effect of historical processes independent of morphological traits. Our findings reinforce the importance of evolutionary history and ecological processes in imprinting patterns of interaction niche overlap.     

Predictors of long-distance dispersal in the Siberian flying squirrel

During dispersal the distances moved differ between individuals. The evolutionary causes of dispersal rate are much studied, for example, it is observed that dispersal is often a condition- and phenotype-dependent strategy. However, more empirical information is needed on factors affecting the dispersal distance. We study factors behind dispersal distance in the juvenile Siberian flying squirrel. The longer dispersing individuals abandoned natal site earlier in the season and were larger, perhaps being born earlier, than shorter dispersing individuals. These patterns did not hold between same-sex siblings, indicating that the early long-distance dispersal was more a between than a within-litter related phenomenon. Our results indicate differences between litters that are related to dispersal strategies of individuals. In flying squirrels, long-distance dispersal is not merely a secondary effect of short-distance dispersal. Instead, the distribution of dispersal distance is affected by factors enhancing long-distance dispersal.     

Three-dimensional structure of the central mitotic spindle of Diatoma vulgare

Central mitotic spindles in Diatoma vulgare have been investigated using serial sections and electron microscopy. Spindles at both early stages (before metaphase) and later stages of mitosis (metaphase to telophase) have been analyzed. We have used computer graphics technology to facilitate the analysis and to produce stereo images of the central spindle reconstructed in three dimensions. We find that at prometaphase, when the nuclear envelope is dissassembling, the spindle is constructed from two sets of polar microtubules (MTs) that interdigitate to form a zone of overlap. As the chromosomes become organized into the metaphase configuration, the polar MTs, the spindle, and the zone of overlap all elongate, while the number of MTs in the central spindle decreases from greater than 700 to approximately 250. Most of the tubules lost are short ones that reside near the spindle poles. The previously described decrease in the length of the zone of overlap during anaphase central spindle elongation is clearly demonstrated in stereo images. In addition, we have used our three- dimensional data to determine the lengths of the spindle MTs at various times during mitotis. The distribution of lengths is bimodal during prometaphase, but the short tubules disappear and the long tubules elongate as mitosis proceeds. The distributions of MT lengths are compared to the length distributions of MTs polymerized in vitro, and a model is presented to account for our findings about both MT length changes and microtubule movements.     

DNA条形码技术在田间常见蓟马种类识别中的应用

蓟马类害虫种类多、 体型小, 传统的形态学鉴定方法难以快速准确识别。本研究利用DNA条形码通用型引物, 以我国田间常见的25种蓟马为靶标扩增其线粒体DNA细胞色素C氧化酶亚基Ⅰ (mitochondrial cytochrome c oxidase subunit Ⅰ gene, mtDNA COⅠ) 基因 (约650 bp), 通过对靶标片段碱基序列的测序及比对分析, 以邻接法 (NJ法) 构建系统发育树, 并以Kimura双参数模型计算种内、 种间遗传距离。结果表明： 聚类分析与形态学鉴定结果一致, 表现为较长的种间分支和较短的种内分支, 每个单系分支对应一个物种, 同一物种不同单倍型的最初分支自展值均为100%。25种蓟马的种内平均遗传距离为0.0027, 种间平均遗传距离为0.2757, 种间遗传距离为种内遗传距离的102.1倍; 而且种内、 种间遗传距离没有重叠区域。结果说明基于COⅠ基因的DNA条形码技术可以用于不同种类蓟马的快速准确鉴别。     

Dynamic spatial partitioning and coexistence among tall grass grazers in an African savanna

Competitive relationships among mobile animals may be expressed through dynamically changing spatial relationships over different time frames. Less common species that are apparently inferior competitors may be able to coexist with more abundant species by concentrating in regions of the landscape little utilized by the former at spatio‐temporal scales from annual or seasonal ranges to the specific foraging localities exploited at different stages of the annual cycle. Spatial relationships may be influenced further by dependencies on other resources, predation risks and facilitatory interactions under certain conditions. Our study aimed to determine whether competition with more abundant zebra and buffalo restricted the abundance of sable antelope in a region where these three tall‐grass grazers overlapped in their herd distributions. We tracked the simultaneous movements of animals representing herds of these species over two dry seasons and one wet season using GPS‐GSM collars, and estimated seasonal or monthly range extents and their overlap. We also compared daily separation distances between these animals against the null pattern expected if their movements had been independent, and assessed how prior grazing by buffalo influenced the subsequent use of these localities by sable. The range of the sable herd was mostly separated from the seasonal range of the buffalo herd during the late dry season of 2006 and throughout the dry season of 2007. Seasonal home ranges of zebra herds overlapped partially with the range of the sable herd during most of the year. Even during times when their ranges overlapped, sable were rarely recorded within <1 km of the buffalo herd. Prior grazing by buffalo beyond a threshold level inhibited later use of these localities by sable, but the sable were nevertheless able to exploit places that were little utilized by buffalo at that time. Sable were less able to evade overlap with the small, mobile zebra herds, and hence more vulnerable to competitive exclusion by zebra than by buffalo. Our findings demonstrate how less abundant species can restrict competition from more abundant competitors through dynamic spatial partitioning in regions where their home ranges overlap.     

Geometrical factors influencing muscle force development. I. The effect of filament spacing upon axial forces.

The influence of geometry on the force and stiffness measured during muscle contraction at different sarcomere lengths is examined by using three specific models of muscle cross-bridge geometry which are based upon the double-hinge model of H. E. Huxley (Science [Wash. D.C.]. 1969, 164:1356-1366) extended to three dimensions. The force generated during muscle contraction depends upon the orientation of the individual cross-bridge force vectors and the distribution of the cross-bridges between various states. For the simplest models, in which filament separation has no effect upon cross-bridge distribution, it is shown that changes in force vectors accompanying changes in myofilament separation between sarcomere lengths 2.0 and 3.65 microgram in an intact frog skeletal muscle fiber have only a small effect upon axial force. The simplest models, therefore, produce a total axial force proportional to the overlap between the actin and myosin filaments and independent of filament separation. However, the analysis shows that it is possible to find assumptions that produce a cross-bridge model in which the axial force is not independent of filament spacing. It is also shown that for some modes of attachment of subfragment-1 (S1) to actin the azimuthal location of the actin site is important in determining the axial force. A mode of S1 attachment to actin similar to that deduced by Moore et al. (J. Mol. Biol., 1970, 50:279-294), however, exhibits rather constant cross-bridge behavior over a wide range of actin site location.