MapMi: automated mapping of microRNA loci

Background  

A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. However, miRBase focuses on those species for which miRNAs have been directly confirmed. Secondly, specific miRNAs or their loci are sometimes not annotated even in well-covered species. We sought to address this problem by developing a computational system for automated mapping of miRNAs within and across species. Given the sequence of a known miRNA in one species it is relatively straightforward to determine likely loci of that miRNA in other species. Our primary goal is not the discovery of novel miRNAs but the mapping of validated miRNAs in one species to their most likely orthologues in other species.     

Dispersal ability of island endemic plants: What can we learn using multiple dispersal traits?

Island endemic species are expected to have lower dispersal ability than their non-endemic congeners. Several studies have demonstrated differences in diaspore morphology between endemic species and their non-endemic congeners. It is, however, relatively difficult to translate the differences in morphology of the diaspores into differences in dispersal ability. To avoid this problem, we measured directly dispersal values (anemo-, hydro-, exozoo- and endozoo-chory) of 27 pairs of closely related endemic and non-endemic species from Canary Islands. We did not explicitly support the hypothesis about the loss of dispersal ability of island species. The comparison of pairs of endemic and non-endemic species showed the reduction in dispersal potential only for endozoochory. In many cases, endemic species had, in fact, the same or better dispersal ability than their non-endemic congeners. Higher dispersal ability of endemic species could have been evolved as a consequence of species subsequent dispersal to neighboring islands. As a support for this we found that the endemic species dispersing better than their non-endemic congeners also occupy more islands within the archipelago. We conclude that reduction of dispersal ability of species on islands may not be as general as previously expected and we need to take into account multiple species traits to understand the possible evolution of species dispersal potential.     

The origin of a mutualism: a morphological trait promoting the evolution of ant-aphid mutualisms

Mutualisms are mutually beneficial interactions between species and are fundamentally important at all levels of biological organization. It is not clear, however, why one species participates in a particular mutualism whereas another does not. Here we show that pre-existing traits can dispose particular species to evolve a mutualistic interaction. Combining morphological, ecological, and behavioral data in a comparative analysis, we show that resource use in Chaitophorus aphids (Hemiptera: Aphididae) modulates the origin of their mutualism with ants. We demonstrate that aphid species that feed on deeper phloem elements have longer mouthparts, that this inhibits their ability to withdraw their mouthparts and escape predators and that, consequently, this increases their need for protection by mutualist ants.     

Coexistence in a metacommunity: the competition-colonization trade-off is not dead

The competition–colonization trade-off model is often used to explain the coexistence of species. Yet its applicability has been severely criticized, mainly because the original model assumed a strict competitive hierarchy of species and did not allow for any preemptive effect. We considered the impact of relaxing both of these limitations on coexistence. Relaxing trade-off intensity makes coexistence less likely and introduces a minimum colonization rate below which any coexistence is impossible. Allowing for preemption introduces a limit to dissimilarity between species. Surprisingly, preemption does not impede coexistence as one could presume from previous studies, but can actually increase the likelihood of coexistence. Its effect on coexistence depends on whether or not species in the regional pool are strongly limited in their colonization ability. Preemption is predicted to favour coexistence when: (i) species are not strongly limited in their colonization ability; and (ii) the competitive trade-off is not infinitely intense.     

The influence of phylogeny and ecology on root,shoot and plant ionomes of 14 native Brazilian species

The ionome is the elemental composition of a living organism, its tissues, cells or cell compartments. The ionomes of roots, stems and leaves of 14 native Brazilian forest species were characterised to examine the relationships between plant and organ ionomes and the phylogenetic and ecological affiliations of species. The null hypothesis that ionomes of Brazilian forest species and their organs do not differ was tested. Concentrations of mineral nutrients in roots, stems and leaves were determined for 14 Brazilian forest species, representing seven angiosperm orders, grown hydroponically in a complete nutrient solution. The 14 species could be differentiated by their ionomes and the partitioning of mineral nutrients between organs. The ionomic differences between the 14 species did not reflect their phylogenetic relationships or successional ecology. Differences between shoot ionomes and root ionomes were greater than differences in the ionome of an organ when compared among genotypes. In conclusion, differences in ionomes of species and their organs reflect a combination of ancient phylogenetic and recent environmental adaptations.     

Knowledge,perceptions and willingness to control designated invasive tree species in urban household gardens in South Africa

Many biological invasions result in negative impacts on the environment and human livelihoods, but simultaneously some also provide benefits that are valued differently by various stakeholders. To inform policy and management of invasive species it is important to assess landowners’ and broader society’s knowledge and perceptions of invasive species, something which is lacking in many contexts, especially in urban settings. In this study we interviewed 153 householders living in a medium-sized South African town who had declared invasive alien trees in their gardens. Less than half of the respondents could identify the invasive tree on their property and only one-third knew that it was an invasive alien species. There was a positive association between income and education levels with exposure to media about invasive alien species and respondents’ ability to identify the species and name any other invasive alien tree species. Knowledge levels were unequal across species. Amongst those who knew the tree was an invasive alien species, reasons why they retained it in their gardens included that it would be costly or too much effort to remove, they liked the tree, that it was not causing any harm and that the property was rented and so its removal was not their responsibility. However, the majority of people (83 %) were willing to have it removed from their garden if done for free by appropriate agencies, which is promising for compliance with new regulations on invasive species implemented at the end of 2014 in South Africa. The results also highlight the need for targeted and appropriate education and awareness programs amongst urban householders on invasive alien species, relevant legislation and their obligations.     

Island biogeography of Corsican birds: some trends

The species composition, species richness, and the general characteristics of the Corsican bird fauna are compared to those of similar French mainland areas. Species richness on Corsica is approximately 30% lower than on similar-sized reference areas on the mainland. A comparative study of the species composition Indicates that species impoverishment is not evenly distributed among different species groups. These groups were defined on three levels: taxonomical, biogeographical, and ecological. The sea bird fauna appears not to be impoverished. Freshwater and anthropophileous bird species groups show only little impoverishment, which is to be related to their good dispersal ability as a consequence of the discontinuous distribution of their habitats even on the mainland. The mainland forest species group is one of the most impoverished, but mainland forest species having colonised Corsica show important habitat expansion and increased densities on the island. The sedentarity of these species and particular features of the Corsican environment are proposed as explanations.     

Infusing considerations of trophic dependencies into species distribution modelling

Community ecology involves studying the interdependence of species with each other and their environment to predict their geographical distribution and abundance. Modern species distribution analyses characterise species‐environment dependency well, but offer only crude approximations of species interdependency. Typically, the dependency between focal species and other species is characterised using other species’ point occurrences as spatial covariates to constrain the focal species’ predicted range. This implicitly assumes that the strength of interdependency is homogeneous across space, which is not generally supported by analyses of species interactions. This discrepancy has an important bearing on the accuracy of inferences about habitat suitability for species. We introduce a framework that integrates principles from consumer–resource analyses, resource selection theory and species distribution modelling to enhance quantitative prediction of species geographical distributions. We show how to apply the framework using a case study of lynx and snowshoe hare interactions with each other and their environment. The analysis shows how the framework offers a spatially refined understanding of species distribution that is sensitive to nuances in biophysical attributes of the environment that determine the location and strength of species interactions.     

生产力与生物多样性关系研究进展

生物多样性与生态系统的功能的关系已经成为人类社会面临的一个重大科学问题。本文简要介绍了生产力与生物多样性的概念和研究背景,综述了生产力与物种多样性关系研究的最新进展与争论：1．是物种多样性还是物种特性或物种组成决定生态系统的功能,目前还没有一致的结论;2．生产力与物种多样性关系的尺度效应极其明显,深刻理解和把握生态学尺度和尺度效应有望成为解析生产力与物种多样性关系的突破口：3．不能只保护所谓的关键种,考虑到生态系统的功能很大程度上依赖于受各式各样物种影响的各种不同的过程,尽最大可能保护最大的多样性,才是谨慎而明智的：4．由于自然生态系统极大的复杂性,生产力与物种多样性关系并没有一般的模式。在对已有成果进行综合分析的基础上,对生产力与物种多样性关系研究中亟待解决的区别物种特性与物种多样性问题、尺度问题、实验设计问题进行了探讨,并对未来的发展方向进行了展望。     

Evolution of multiple components of virulence in Drosophila-nematode associations

Abstract.— Virulence is of central importance in host-parasite interactions, yet little is known about how it changes over extended evolutionary periods. In this study, all four species in the testacea species group of Drosophila were experimentally infected with sympatric and allopatric nematodes in the Howardula aoronymphium species complex, and the effect of parasite infection on three components of host fitness was determined. The Drosophila species show striking differences in their responses to infection, with reductions reaching 80% in adult lifespan, 100% in female fertility, and 90% in male fertility. Female sterility appears to be determined by the host; species that are sterilized by their local nematodes are also sterilized by the other allopatric nematodes in the H. aoronymphium complex. Host species that are not sterilized by their local parasite are not sterilized by other nematodes in the complex. In contrast, reductions in host adult lifespan and male fertility depend on both the host and the parasite. Whereas all nematodes reduced the survival of their local host species equally (about 40–45%), survival of two host species was drastically reduced (about 80%) when infected with an allopatric parasite. Thus, virulence is evolutionarily labile in associations between Drosophila testacea group species and their Howardula parasites. The data suggest that changes in the sterility component of virulence are due primarily to host evolution, whereas changes in the host mortality component are due in large part to parasite evolution.     

Weed species and weed communities

Summary With weeds as with many plant species the main or first level factor determining the area of distribution is a (complex) climatic one. As they have an artificially enlarged area of distribution, they have a huge border area (in an ecological sense), where the climate is not optimal for them, and where they have a narrow ecological and sociological amplitude and are especially sensitive to some measures of modern intensified agriculture. In their northern border areas species of southern origin are restricted to calcarcous substrates and to agrestal and finally ruderal communities, while in their optimal climate they are indifferent to that soil factor and able to compete with other species even in natural vegetation types. Species presumably of origin in atlantic areas are restricted with increasing continentality to very poor and acid soils, as they cannot compete with other species on better sites any more, because of their physiological properties. Thus weed distribution demonstrates the complicated reaction of plant species to the complexes of soil-climatic factors and to the competition of other species. As far as weeds are concerned, species may be only relatively calciphilous, but genuinely calcifuge species, the control being climatic in the former case and physiological in the second.The measures of modern agriculture bring about a gradual extinction of sensitive species from the limit of their range towards their centre of distribution, where they can find refuge habitats in the natural vegetation. The sensitivity of such species (also against herbicides) seems to increase towards their limits. Resistant species occur with increasing densities after the removal of their competitors. In addition, they are able to enlarge their area and to invade sites, where they had not been able to compete before, or sites where they could not previously bear the environmental conditions together with the competition of the rich weed flora.As the complex climatic gradients responsible for the ranges of weed species show smooth transitions, the alteration of species composition in weed communities is also a gradual one. This is one of the problems of weed phytosociology briefly discussed.Nomenclature follows Ehrendorfer (1973), Phytosociological units according to Westhoff & Den Held (1969).Contribution to the Symposium on Plant Species and Plant communities, held at Nijmegen, 11–12 November 1976, on the occasion of the 60th birthday of Professor Victor Westhoff.Field studies were partly supported by a grant of the Austrian Federal Ministry of Agriculture and Forestry.     

基于XML的物种属性构建系统

用PowerBuilder9．0开发了一个基于XML的物种及其属性构建系统,利用该系统可以方便的构建一个物种属性,并可以对该物种属性进行解析翻译。利用该系统以物种毛白杨作为实例进行构建,结果表示：该系统操作简便、构建灵活、能解析、方便读取、实用有效,对物种及其属性能够很好的描述,方便物种属性的管理。     

Three species of Hypomyces growing on basidiomata of Stereaceae

Of the eight species of Hypomyces that occur on basidiomata of Stereum species, only H. sympodiophorus grows exclusively on members of this genus. Morphologically similar fungi were found on species of Xylobolus, a genus closely related to Stereum. These are described as two new species of Hypomyces: H. thailandicus, collected on Xylobolus cf. illudens in Thailand; and H. xyloboli, on X. frustulatus and X. subpileatus in the eastern United States. These three species are unusual in Hypomyces because of their almost indistinguishable anamorphs. In parsimony analysis of LSU nuclear rDNA sequences, the three species growing only on Stereaceae do not form a monophyletic group but their constrained monophyly is not rejected either. A morphologically similar anamorphic species, Sibirina gamsii, included in the study, is transferred to the genus Cladobotryum.     

外来入侵杂草的生物防治及生防因子对本地非目标种的影响

随着生物入侵所引起的生态及经济问题日益严重,对有害入侵生物的防治问题也备受人们关注。生物防治因具有持续、高效、安全等优点,已成为防治有害入侵生物的重要方法。传统生防是防治有害入侵杂草的一种重要方法。在简单介绍生物防治的基础上,重点阐述了传统生物防治的理论基础——天敌逃逸假说,生防因子对外来人侵种的影响及其对本地非目标种的直接和间接效应,并针对这些问题,对我国开展生物防治工作提出几点建议。     

Learning fine-tunes a specific response of nestlings to the parental alarm calls of their own species

Parent birds often give alarm calls when a predator approaches their nest. However, it is not clear whether these alarms function to warn nestlings, nor is it known whether nestling responses are species-specific. The parental alarms of reed warblers, Acrocephalus scirpaceus ("churr"), dunnocks, Prunella modularis ("tseep"), and robins, Erithacus rubecula ("seee") are very different. Playback experiments revealed that nestlings of all three species ceased begging only in response to conspecific alarm calls. These differences between species in response are not simply a product of differences in raising environment, because when newly hatched dunnocks and robins were cross-fostered to nests of the other two species, they did not develop a response to their foster species' alarms. Instead, they still responded specifically to their own species' alarms. However, their response was less strong than that of nestlings raised normally by their own species. We suggest that, as in song development, a neural template enables nestlings to recognize features of their own species' signals from a background of irrelevant sounds, but learning then fine-tunes the response to reduce recognition errors.     

Is parasitism of numerically dominant species in macrolepidopteran assemblages independent of their abundance?

Refuge theory proposes that a determinant of species richness (and percent parasitism) is the presence of host refuges. Plant structural refuges are good predictors of species richness for endophytic herbivores, but not for exophytic herbivores. For exophytic herbivores other traits such as relative abundance may provide refuge from parasitism. Using unbiased data on both relative abundance and larval parasitism of species in macrolepidopteran assemblages we tested the null hypothesis that percent parasitism was independent of abundance. Numerically subdominant species do not gain refuge from parasitism by persisting at low abundance. Parasitism was not different from what would be expected based on their numbers. Among numerically dominant species there was, nevertheless, a significant positive association between abundance and parasitism rate. However, dominant herbivores displayed high levels of parasitism even in the years when their abundance was low relative to other years. This suggests that dominant species may possess other traits that enhance their susceptibility to parasitoids.     

果蝇亚群中六个种的求爱歌的研究：对ipi作用的探究

据认为果蝇求爱歌的脉冲间隔(ipi)在种特异性配偶认识系统(SMRS)中起着重要的作用。果蝇D.takahashii亚群中各物种求爱歌的ipi值和种间亲缘关系的相关性如何?迄今尚未见报道。我们测定了此亚群中能饲养存活的6个种的ipi,并用O’Farrell双向电泳方法及杂交实验研究了它们之间的亲缘关系。在近缘种D.takahashii和D.lutescens之间,D.takahashii和D.paralutea之间,D.lutescens和D.paralutea之间,其求爱歌的ipi值,不论平均数或众数都相差甚远。而D.paralutea和D.prostipennis是2个亲缘关系较远的种,两者不能杂交,但其ipi的平均数在统计学上无差异,众数亦很相近。本实验可导出这样的见解:ipi值在不同果蝇种群或亚群的SMRS中的作用可能并不相同。在D.takahashii亚群中ipi值对于杂交成败似乎不起支配性作用。     

The biology and ecology of narrow endemic and widespread plants: a comparative study of trait variation in 20 congeneric pairs

The objective of this study is to examine whether habitat, herbivory and traits related to resource acquisition, resource conservation, reproduction and dispersal differ between narrow endemic plant species and their widespread congeners. We undertook pairwise contrasts of 25 ecological characteristics and biological traits in 20 congeneric pairs of narrow endemic and widespread plant species in the French Mediterranean region. Within each pair, the two species had the same life-form, pollination mode and dispersal mode. Endemic species differed significantly from widespread congeners for a number of attributes. Endemic species occur in habitats on steeper slopes, with higher rock cover and in lower and more open vegetation than their widespread congeners. Endemic species are significantly smaller than widespread species, but show no differences in traits related to resource acquisition (specific leaf area, leaf nitrogen content, maximum photosynthetic rate) or resource conservation (leaf dry matter content). After accounting for their smaller stature, endemic species produce fewer and smaller flowers with less stigma-anther separation and lower pollen/ovule ratios and produce fewer seeds per plant than their widespread congeners. No consistent variation in seed mass and propagule structure was found between congeneric species. Herbivory levels did not differ between congeneric species. Ecological characteristics, notably the occupation of rocky habitats with low aboveground competition, may thus have played an important role in the differentiation of narrow endemic species in the Western Mediterranean. Morphological and ecophysiological traits of narrow endemic species indicate that they are not more stress-tolerant than their widespread congeners. Lower investment in pollen transfer and seed production suggest that local persistence is a key feature of the population ecology of narrow endemic species.     

The relationship between mating system and penis morphology in ischnuran damselflies (Odonata: Goenagrionidae)

Zygopterans belonging to the genus Ischnura are unusual amongst damselflies because of the variety of mate guarding techniques employed by males of different species. The lack of post-copulatory guarding combined with lengthy copulations in one group of ischnuran species suggest that these males guard females in copula. An examination of the accessory penes of species in this group indicates that all but one species have considerable microspination on the distal end (the flagella) of their penes that can function in sperm displacement. The flagella of these species are long and thin compared to those of other ischnurans. This is likely an adaptation to gain access to the spermatheca of the female. Two species tandem guard their mates during ovipositing. These species are the only ischnurans missing a stout pair of basal spines on the penultimate segments of their penes. They have considerable microspination over much of their penes but their flagella are of only moderate length and stout. Ischnurans that do not mate guard have short, stout flagella and most species examined from this group (5 of 7) have litde microspination on their flagella tips. It is proposed that females of these species mate only once and therefore their males do not displace sperm.