南方红豆杉不同居群遗传多样性的RAPD研究

用随机扩增多态性方法对广东、湖南、江西等3省的12个南方红豆杉自然居群进行了基因组DNA多态性分析,从100条引物中共筛选出10个引物,获得RAPD谱带86条,多态性谱带占51％。聚类分析结果表明：南方红豆杉居群间的遗传距离与这些居群的地理分布相关,即相同或相邻产地的居群间的遗传距离较小,不同产地个体间的遗传距离较大。粤北南方红豆杉的9个居群的遗传多样性较低,可能与近年来资源遭到严重破坏,及其生长缓慢、种子萌发率低、成活率不高等原因有关。     

Agroforestry systems conserve species-rich but modified assemblages of tropical birds and bats

Although an increasing number of studies have shown that diverse, multi-strata agroforestry systems can contribute to the conservation of tropical biodiversity, there is still debate about how the biodiversity within agroforestry systems compares to that of intact forest and alternative land uses. In order to assess the relative importance of agroforestry systems for biodiversity conservation, we characterized bat and bird assemblages occurring in forests, two types of agroforestry systems (cacao and banana) and plantain monocultures in the indigenous reserves of Talamanca, Costa Rica. A total of 2,678 bats of 45 species were captured, and 3,056 birds of 224 species were observed. Agroforestry systems maintained bat assemblages that were as (or more) species-rich, abundant and diverse as forests, had the same basic suite of dominant species, but contained more nectarivorous bats than forests. Agroforestry systems also contained bird assemblages that were as abundant, species-rich and diverse as forests; however the species composition of these assemblages was highly modified, with fewer forest dependent species, more open area species and different dominant species. The plantain monocultures had highly modified and depauperate assemblages of both birds and bats. Across land uses, bird diversity and species richness were more closely correlated with the structural and floristic characteristics than were bats, suggesting potential taxon-specific responses to different land uses. Our results indicate that diverse cacao and banana agroforestry systems contribute to conservation efforts by serving as habitats to high numbers of bird and bat species, including some, but not all, forest-dependent species and species of known conservation concern. However, because the animal assemblages in agroforestry systems differ from those in forests, the maintenance of forests within the agricultural landscape is critical for conserving intact assemblages at the landscape level.     

A Hybrid Pairwise Likelihood Method

A modification to the pairwise likelihood method is proposed,which aims to improve the estimation of the marginal distributionparameters. This is achieved by replacing the pairwise likelihoodscore equations, for estimating such parameters, by the optimallinear combinations of the marginal score functions. A furtheradvantage of the proposed estimator of marginal parameters,over pairwise likelihood, is that it is robust to misspecificationof the bivariate distributions as long as the univariate marginaldistributions are correctly specified. While alternating logisticregression can be seen as a special case of the proposed method,it is shown that an existing generalization of alternating logisticregression applicable to ordinal data is not the same as andis inferior to the proposed method because it replaces certainconditional densities by pseudodensities that assume workingindependence. The fitting of the multivariate negative binomialdistribution is another scenario involving intractable likelihoodthat calls for the use of pairwise likelihood methods, and thesuperiority of the modified method is demonstrated in a simulationstudy. Two examples, based on the analyses of salamander matingand patient-controlled analgesia data, demonstrate the usefulnessof the proposed method. The possibility of combining optimallythe pairwise, rather than marginal, scores is also consideredand its difficulty and potential are discussed.     

Random amplified polymorphic DNA (RAPD) analysis in Indian mung bean (Vigna radiata (L.) Wilczek) cultivars

Greengram [Vigna radiata (L.) Wilczek], also known as mung bean, widely cultivated in a large number of countries, is an important pulse crop of Asia and is considered one of the ancestral species of the genus Vigna. Since yields of greengram have remained low across subtropical and tropical Asia, it is important to estimate genetic diversity in existing cultivars in order to see if the lack of genetic variability might be a constraining factor. In this study, 32 Indian cultivars of greengram were subjected to random amplified polymorphic DNA (RAPD) analysis using 21 decamer primers. A total of 267 amplification products were formed at an average of 12.71 per primer with an overall polymorphism of 64%. The extent of polymorphism was moderate to low. Jaccard similarity coefficient values ranged from 0.65 to 0.92. The cluster analysis resulted in mainly three clusters revealing greater homology between cultivars released from the same source. The results of principal components analysis also substantiated this conclusion. The close genetic similarity between the cultivars could be explained due to the high degree of commonness in their pedigrees. The narrow genetic base of the greengram cultivars revealed in the present analysis emphasises the need to exploit the large germplasm collections having diverse morphoagronomic traits in cultivar improvement programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Diversity and phenology of hoverflies (Diptera: Syrphidae) in pine forests (Pinus halepensis Miller) of Algeria

Hoverflies are good indicators of ecosystem integrity, especially in drylands. However, the key factors explaining hoverfly diversity in North African forest ecosystems are still not addressed. The current study provides data on the diversity, structure and functional trophic groups (FTG) of the hoverfly community in Aleppo pine forests under a semi-arid climate in northeastern Algeria. Using an entomological net, hoverflies were sampled weekly during 2008–2009. Alpha and beta-diversity of hoverflies and functional trophic group (FTG) were analyzed using several parameters and indices (e.g. species composition, richness, occurrence, diversity, estimations, similarity, etc.). In total, 602 individuals of 21 species were collected with a constant species (Eupeodes corollae) and four common species (Episyrphus balteatus, Chrysotoxum intermedium, Eristalis arbustorum and Eristalis tenax). Most species (17) occurred accidentally or very accidentally in samples. The highest diversity was recorded during spring, corresponding to the flowering season of most understory plant species. Seasonal rarefaction and extrapolation curves indicated that the expected species richness would be higher in autumn and spring compared to summer and winter. The spectrum of FTG ranked predators first with 52.4% of species, followed by saprophagous (42.8%) and then phytophagous (4.8%) species. Hoverfly communities showed high taxonomic richness and alpha-diversity all over the year, with peaks during spring that coincides with flowering period of most plant species of the forest understorey and favourable climatic conditions.     

Neotropical seasonally dry forests and Quaternary vegetation changes

Seasonally dry tropical forests have been largely ignored in discussions of vegetation changes during the Quaternary. We distinguish dry forests, which are essentially tree‐dominated ecosystems, from open savannas that have a xeromorphic fire‐tolerant, grass layer and grow on dystrophic, acid soils. Seasonally dry tropical forests grow on fertile soils, usually have a closed canopy, have woody floras dominated by the Leguminosae and Bignoniaceae and a sparse ground flora with few grasses. They occur in disjunct areas throughout the Neotropics. The Chaco forests of central South America experience regular annual frosts, and are considered a subtropical extension of temperate vegetation formations. At least 104 plant species from a wide range of families are each found in two or more of the isolated areas of seasonally dry tropical forest scattered across the Neotropics, and these repeated patterns of distribution suggest a more widespread expanse of this vegetation, presumably in drier and cooler periods of the Pleistocene. We propose a new vegetation model for some areas of the Ice‐Age Amazon: a type of seasonally dry tropical forest, with rain forest and montane taxa largely confined to gallery forest. This model is consistent with the distributions of contemporary seasonally dry tropical forest species in Amazonia and existing palynological data. The hypothesis of vicariance of a wider historical area of seasonally dry tropical forests could be tested using a cladistic biogeographic approach focusing on plant genera that have species showing high levels of endemicity in the different areas of these forests.     

Segmental conformational disorder and dynamics in the intrinsically disordered protein α-synuclein and its chain length dependence

Conformational ensembles of fully disordered natural polypeptides represent the starting point of protein refolding initiated by transfer to folding conditions. Thus, understanding the transient properties and dimensions of such peptides under folding conditions is a necessary step in the understanding of their subsequent folding behavior. Such ensembles can also undergo alternative folding and form amyloid structures, which are involved in many neurological degenerative diseases. Here, we performed a structural study of this initial state using time-resolved fluorescence resonance energy transfer analysis of a series of eight partially overlapping double-labeled chain segments of the N-terminal and NAC domains of the α-synuclein molecule. The distributions of end-to-end distance and segmental intramolecular diffusion coefficients were simultaneously determined for eight labeled chain segments. We used the coefficient of variation, C_v, as a measure of the conformational heterogeneity (i.e., structural disorder). With the exception of two segments, the C_vs were characteristic of a fully disordered state of the chain. Subtle deviations from this behavior at the segment labeled in the NAC domain and the segment at the N termini reflected subtle conformational bias that might be related to the initiation of transition to amyloid aggregates. The chain length dependence of the mean segmental end-to-end distance followed a power law as predicted by Flory, but the dependence was steeper than previously predicted, probably due to the contribution of the excluded volume effect, which is more dominant for shorter-chain segments. The observed intramolecular diffusion coefficients (< 10 to ∼ 25 ?²/ns) are only an order of magnitude lower than the common diffusion coefficients of low molecular weight probes. This diffusion coefficient increased with chain length, probably due to the cumulative contributions of minor bond rotations along the chain. These results gave us a reference both for characteristics of a natural unfolded polypeptide at the moment of initiation of folding and for detection of possible initiation sites of the amyloid transition.     

3种不同来源侧耳品种亲缘关系差异化分析

采取拮抗实验、酯酶同工酶、基因组进行多态性分析(RAPD)、内部转录间隔区序列(ITS)对来源不同的特大凤尾菇(Pleurotus sajor-caju)、夏秀990(Pleurotus geesteranus)和黑平A3三个侧耳品种的亲缘关系进行了对比分析。实验结果表明:供试的3个侧耳品种从形态学水平、蛋白质水平和分子水平上看,其品种间亲缘关系界定具有一致性。表现为特大凤尾菇与夏秀990的亲缘关系较近,与黑平A3的亲缘关系较远,夏秀990与黑平A3亲缘关系较远。本研究从不同的水平,为食用菌菌种属间亲缘关系的鉴定提供了综合分析方法,对区分同种异名、杂交亲本选择以及判定杂交结果具有指导意义。