Speciation and periodic restricted environments. The case of genus Ononis L. (subsections Natrix and Viscosae)

The morpho–environmental similarity between subsections Natrix and Viscosae has been pointed out as the reason for the genetic complexity of these groups of taxa. Based on this characterization a question emerges: could a very recent ongoing evolutionary process explain that morpho–environmental similarity? ISSR and cpSSR amplifications for 45 specimens belonging to taxa of Natrix and Viscosae subsections were developed, along their biogeographic distribution areas. Twenty-nine haplotypes were detected in the biogeographic area of both subsections, 79% were exclusive haplotypes, but the rest is shared between subsections Natrix and Viscosae species. Could that haplotype sharing be the result of potential hybridization between these taxa? Do current environmental conditions restrict the gene flow among taxa? The combination of ancestral genetic polymorphism, introgression, coalescence processes and periodic restricted environments (PRE) by glacial–interglacial environmental dynamics were discussed to explain the relevant percentage of exclusive haplotypes detected, as well as the persistence of shared haplotypes. These results are in accordance with the morpho–environmental proximity previously described for both subsections.     

Trait‐based approach confirms the importance of propagule limitation and assembly rules in old‐field restoration

Community assembly theory is suggested as a guiding principle for ecological restoration to help understand the mechanisms that structure biological communities and identify where restoration interventions are needed. We studied three hypotheses related to propagule limitation, stress‐dominance, and limiting similarity concepts in community assembly in a restoration field experiment with a trait‐based null model approach. The experiment aimed to assist the recovery of sand grassland on former arable land in the Kiskunság, Pannonian biogeographic region, Europe. Treatments included initial seeding of five grassland species, carbon amendment, low‐intensity mowing, and combinations in 1 m by 1 m plots in three old fields from 2003 to 2008. The distribution of 10 individual plant traits was compared to the null model and the effect of time and treatments were tested with linear mixed effect models. Initial seeding had the most visible impact on species and trait composition confirming propagule limitation in grassland recovery. Reducing nutrient availability through carbon amendment strengthened trait convergence for length of flowering as expected based on the stress‐dominance hypothesis. Mowing changed trait divergence to convergence for plant height with a strengthening impact with time, supporting our hypothesis of increasing dominance of limiting similarity with time. Our results support the idea that community assembly is simultaneously influenced by propagule limitation and multiple trait‐based processes that act through different traits. The limited impact of manipulating environmental filtering and limiting similarity compared to seeding, however, supports the view that only targeting the dispersal and environmental filters in parallel would improve restoration outcome.     

Diversity and host associations of dipteran insects exploiting fungal fruiting bodies in Hokuriku,central Japan

To clarify the diversity and host associations of dipteran insects exploiting fungal fruiting bodies, we collected fruiting bodies at 18 localities in Hokuriku region, central Japan, from 2012 to 2015 and examined them for the emergence of insects. In total, 14,107 dipteran individuals belonging to 20 families emerged from fungi of 8 orders, 25 families, 49 genera and 129 species. Approximately 79% of dipteran individuals belonged to three families, Phoridae, Muscidae and Drosophilidae. The faunal similarity at the family level was relatively high between central (warm‐temperate) and northern (cool‐temperate) areas of Japan. However, the species composition of Drosophilidae was much different between central and northern Japan. The difference in the species composition was discussed in relation to the climatic conditions and fungal flora. None of the species from Drosophilidae, Phoridae, Muscidae, Mycetophilidae, Lonchaeidae and Chloropidae were specialists (they exploited more than one species of fungi), but they showed differences their fungi preference. Adults of some families, especially Drosophilidae, were frequently collected from fruiting bodies, but those of other families were seldom collected, probably reflecting differences in adult feeding ecology.     

几种氧代丙酸化合物在诱捕白纹伊蚊中的应用

为了从氧代丙酸化合物中筛选出对白纹伊蚊Aedes albopictus具有良好引诱效果的化合物,采用陷阱诱捕法分别测定了丙酮酸（α-氧代丙酸）、3-甲氧基-2-甲基-3-氧代丙酸、3-(苄氧基)-3-氧代丙酸和3-氨基-3-氧代丙酸4种氧代丙酸化合物及丙酸对白纹伊蚊成虫的诱捕效果。结果表明,在供试的5种化合物中,α-氧代丙酸、3-甲氧基-2-甲基-3-氧代丙酸和3-(苄氧基)-3-氧代丙酸3种氧代丙酸化合物及丙酸的诱捕效果显著,同剂量的各化合物对白纹伊蚊的诱蚊效果依次是3-甲氧基-2-甲基-3-氧代丙酸>3-(苄氧基)-3-氧代丙酸>α-氧代丙酸=丙酸。相同质量α-氧代丙酸∶3-(苄氧基)-3-氧代丙酸=1∶1至1∶2的配方比,具有协同增效作用,平均累计诱捕量均显著优于单组分α-氧代丙酸、3-(苄氧基)-3-氧代丙酸和对照纯水（P<0.05）。其中最优配方比是α-氧代丙酸∶3-(苄氧基)-3-氧代丙酸=1∶2,平均累计诱捕量比单组分α-氧代丙酸增加45.45%,比单组分3-(苄氧基)-3-氧代丙酸增加32.33%和比对照纯水增加73.11%（P<0.05）。现场诱蚊试验结果表明,根据相似相溶原理将液体的氧代丙酸（α-氧代丙酸、3-甲氧基-2-甲基-3-氧代丙酸）分别与固体的氧代丙酸（3-(苄氧基)-3-氧代丙酸）混配并结合陷阱诱捕器,能够显著提高对白纹伊蚊的持效性及诱捕数量（混合物60 d的累计诱蚊总数量是单组分的1.28~2.15倍）。研究结果为进一步开发适用于家居办公环境中使用的诱蚊剂提供了研究基础。     

Eco‐evolutionary experience in novel species interactions

A better understanding of how ecological novelty influences interactions in new combinations of species is key for predicting interaction outcomes, and can help focus conservation and management efforts on preventing the introduction of novel organisms or species (including invasive species, GMOs, synthetic organisms, resurrected species and emerging pathogens) that seem particularly ‘risky’ for resident species. Here, we consider the implications of different degrees of eco‐evolutionary experience of interacting resident and non‐resident species, define four qualitative risk categories for estimating the probability of successful establishment and impact of novel species and discuss how the effects of novelty change over time. Focusing then on novel predator–prey interactions, we argue that novelty entails density‐dependent advantages for non‐resident species, with their largest effects often being at low prey densities. This is illustrated by a comparison of predator functional responses and prey predation risk curves between novel species and ecologically similar resident species, and raises important issues for the conservation of endangered resident prey species.     

Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism

Kinetin, a cytokinin which promotes seed germination by inhibiting the action of abscisic acid, is an important molecule known to trigger various molecular mechanisms by interacting with an array of proteins shown from experimental observations in various model organisms. We report here the prediction of most probable protein targets of kinetin from spinach proteome using in silico approaches. Inverse docking and ligand-based similarity search was performed using kinetin as molecule. The former method prioritized six spinach proteins, whereas the latter method provided a list of protein targets retrieved from several model organisms. The most probable protein targets were selected by comparing the rank list of docking and ligand similarity methods. Both of these methods prioritized chitinase as the most probable protein target (ΔG_pred = 5.064 kcal/mol) supported by the experimental structure of yeast chitinase 1 complex with kinetin (PDB: 2UY5) and Gliocladium roseum chitinase complex with 3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione (caffeine; 3G6M) which bears a 3D similarity of 0.43 with kinetin. An in vitro study to evaluate the effect of kinetin on spinach seed germination indicated that a very low concentration of kinetin (0.5 mg/l) did not show a significant effect compared to control in inducing seed germination process. Further, higher levels of kinetin (>0.5 mg/l) constituted an antagonist effect on spinach seed germination. It is anticipated that kinetin may have a molecular interaction with prioritized protein targets synthesized during the seed germination process and reduces growth. Thus, it appears that kinetin may not be a suitable hormone for enhancing spinach seed germination in vitro.

Electronic supplementary material

The online version of this article (doi:10.1007/s12154-015-0135-3) contains supplementary material, which is available to authorized users.     

杂色山雀的婚外父权与配偶间的遗传相容性无关

婚配制度作为一种进化稳定对策是动物对某一环境包括种群内部环境适应的结果。据统计,约92%的鸟类为社会性单配制,但单配制鸟类中很多都存在婚外父权现象,表现出社会性婚配制度与遗传性婚配制度的不一致性。杂色山雀(Parus varius)是一种社会性单配制的小型森林洞巢鸟,其是否存在婚外父权现象至今尚未见报道。通过对杂色山雀进行亲权鉴定以确定其有无婚外父权现象及婚外父权的比例,结果显示:45.45%(20/44)的巢存在婚外父权,14.39%(38/264)的后代为婚外子代,说明杂色山雀具有较高的婚外父权水平。进一步探究其婚外父权的发生原因,结果如下:(1)有、无婚外父权巢的社会性亲本之间的遗传相似性无显著差异(P=0.504);(2)有婚外父权巢中婚内子代和无婚外父权巢中子代的杂合度(P=0.118)以及有婚外父权巢中婚外子代与婚内子代的杂合度(P=0.206)均无显著差异。(3)有婚外父权巢中的婚内子代与婚外子代间8项体征指标比较,差异均不显著(Ps0.05)。综上,社会性单配制杂色山雀婚外父权的发生与配偶间的遗传相容性无关,还有待从其他角度进行探究。     

阿尔泰山南坡种子植物区系特点分析

阿尔泰山脉地处亚洲中部,斜跨中国、俄罗斯、蒙古、哈萨克斯坦四国国境,生态环境良好,植物资源丰富。本文在查阅文献资料的基础上,结合野外实地调查,比较了中国新疆、俄罗斯、蒙古及哈萨克斯坦阿尔泰山野生种子植物的种类、组成及其分布区类型的差异,分析了四地阿尔泰山野生种子植物的相似性与差异性。结果显示:(1)四地阿尔泰山野生种子植物资源丰富,按丰富度大小依次为:俄罗斯阿尔泰山蒙古阿尔泰山中国新疆阿尔泰山哈萨克斯坦阿尔泰山。(2)含1种和2~10种的科和属在四地阿尔泰山的科和属种都具有绝对优势。(3)四地阿尔泰山种子植物科的分布区类型均以世界分布型和北温带分布型为主;在属级水平上,以北温带分布型、旧世界温带分布型、世界分布型和地中海、西亚至中亚分布型为主。(4)四地阿尔泰山种子植物科和属的相似性系数都超过了50%,说明四地阿尔泰山的亲缘关系密切。研究表明,四地阿尔泰山种子植物区系存在一定的差异,中国新疆阿尔泰山对整个阿尔泰山的各个植物区系的接触、混合和特化起桥梁作用。     

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence,full structure,and active site microenvironment similarity

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods.