Tooth and cranial disparity in the fossil relatives of Sphenodon (Rhynchocephalia) dispute the persistent ‘living fossil’ label

The tuatara (Sphenodon punctatus) is the only living representative of Rhynchocephalia, a group of small vertebrates that originated about 250 million years ago. The tuatara has been referred to as a living fossil; however, the group to which it belongs included a much greater diversity of forms in the Mesozoic. We explore the morphological diversity of Rhynchocephalia and stem lepidosaur relatives (Sphenodon plus 13 fossil relatives) by employing a combination of geometric morphometrics and comparative methods. Geometric morphometrics is used to explore cranium size and shape at interspecific scale, while comparative methods are employed to test association between skull shape and size and tooth number after taking phylogeny into account. Two phylogenetic topologies have been considered to generate a phylomorphospace and quantify the phylogenetic signal in skull shape data, the ancestral state reconstruction as well as morphological disparity using disparity through time plots (DTT). Rhynchocephalia exhibit a significant phylogenetic signal in skull shape that compares well with that computed for other extinct vertebrate groups. A consistent form of allometry has little impact on skull shape evolution while the number of teeth significantly correlates with skull shape also after taking phylogeny into account. The ancestral state reconstruction demonstrates a dramatic shape difference between the skull of Sphenodon and its much larger Cretaceous relative Priosphenodon. Additionally, DTT demonstrates that skull shape disparity is higher between rather than within clades while the opposite applies to skull size and number of teeth. These results were not altered by the use of competing phylogenic hypotheses. Rhynchocephalia evolved as a morphologically diverse group with a dramatic radiation in the Late Triassic and Early Jurassic about 200 million years ago. Differences in size are not marked between species whereas changes in number of teeth are associated with co‐ordinated shape changes in the skull to accommodate larger masticatory muscles. These results show that the tuatara is not the product of evolutionary stasis but that it represents the only survivor of a diverse Mesozoic radiation whose subsequent decline remains to be explained.     

植物QTL定位方法的研究进展

本文系统地介绍了QTL定位的单一标记分析法、区间作图法以及复合区间作图法、混合显性模型的分析方法,概述了一些主要定位方法的分析原理、存在的主要优缺点。单一标记分析法可以采用方差分析、回归分析或似然比检验的方法分析。区间作图法和复合区间作图法是基于两个相邻标记的QTL定位方法,可采用回归分析或最大似然法分析。复合区间作图法在模型中包括了与其他QTL连锁的标记,可以提高作图的精度和效率。混合线性模型的QTL定位方法可以包括复杂的遗传效应及QTL与环境的互作效应,具有更广阔的应用前景。 Abstract:QTL mapping methods are reviewed for single-marker mapping,interval mapping,composite interval mapping,and mixed-model based method.Statistical approaches along with their properties are discussed for the mapping methods.ANOVA,regression method and likelihood ratio test can be applied in single-marker mapping.Interval mapping and composite interval mapping can be conducted,based on two interval markers,by regression method and maximum likelihood method.Since markers linked with other QTLs are include in the model,composite interval mapping is more precision and powerful.Mapping QTL by mixed-model approaches is more applicable when complicated QTL effects as well as QTL by environment interaction are analyzed.     

Optimizing methods for PCR-based analysis of predation

Molecular methods have become an important tool for studying feeding interactions under natural conditions. Despite their growing importance, many methodological aspects have not yet been evaluated but need to be considered to fully exploit the potential of this approach. Using feeding experiments with high alpine carabid beetles and lycosid spiders, we investigated how PCR annealing temperature affects prey DNA detection success and how post-PCR visualization methods differ in their sensitivity. Moreover, the replicability of prey DNA detection among individual PCR assays was tested using beetles and spiders that had digested their prey for extended times postfeeding. By screening all predators for three differently sized prey DNA fragments (range 116-612 bp), we found that only in the longest PCR product, a marked decrease in prey detection success occurred. Lowering maximum annealing temperatures by 4 °C resulted in significantly increased prey DNA detection rates in both predator taxa. Among the three post-PCR visualization methods, an eightfold difference in sensitivity was observed. Repeated screening of predators increased the total number of samples scoring positive, although the proportion of samples testing positive did not vary significantly between different PCRs. The present findings demonstrate that assay sensitivity, in combination with other methodological factors, plays a crucial role to obtain robust trophic interaction data. Future work employing molecular prey detection should thus consider and minimize the methodologically induced variation that would also allow for better cross-study comparisons.     

Ecological and phylogenetic influence on mandible shape variation of South American caviomorph rodents (Rodentia: Hystricomorpha)

We analyzed mandible shape variation of 17 genera belonging to three superfamilies (Cavioidea, Chinchilloidea, and Octodontoidea) of South American caviomorph rodents using geometric morphometrics. The relative influence of phylogeny and ecology on this variation was assessed using phylogenetic comparative methods. Most morphological variation was concentrated in condylar, coronoid, and angular processes, as well as the diastema. Features potentially advantageous for digging (i.e. high coronoid and condylar processes, relatively short angular process, and diastema) were present only in octodontoids; cavioids showed opposing trends, which could represent a structural constraint for fossorial habits. Chinchilloids showed intermediate features. Genera were distributed in the morphospace according to their classification into superfamilial clades. The phylogenetic signal for shape components was significant along phylogeny, whereas the relationship between mandibular shape and ecology was nonsignificant when phylogenetic structure was taken into account. An early evolutionary divergence in the mandible shape among major caviomorph clades would explain the observed strong phylogenetic influence on the variation of this structure. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 828–837.     

Phosphorus in interstitial water: methods and dynamics

Interstitial (pore) water is important for phosphorus dynamics in limnic ecosystems. This review summarizes the most important processes influencing the generation and transport of pore-water P from, to and within the sediment. Sampling methodology is discussed thoroughly in combination with what little information is available on various P species in the pore water.Pore water P concentrations in various trophic systems and the spatial and temporal distributions are also described. The last sections of the article deal with diffusive P flux calculations and comparison with measured P fluxes. Factors influencing P fluxes, such as adsorption, possible precipitation mechanisms, advection and bioturbation, are discussed.The general conclusion drawn from this review is that pore-water P investigations (concentrations and gradients) are an underestimated ecological tool in studying and describing trophic status, redox conditions, spatial and temporal distribution of P-sediment release, potential precipitation mechanisms on a long-term basis and ground-water inflow areas, as well as lake-water seepage.     

CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)1

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution between genome size and cell volume. We then explored the evolutionary and ecological implications of this evolutionary relationship. Diatom cell volume is an important component of the global carbon cycle; therefore, understanding the mechanisms that drive diatom genome evolution has both evolutionary and ecological importance.     

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

One of the common methods for assessing energy functions of proteins is selection of native or near-native structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all-atom statistical energy functions, DFIRE (distance-scaled, finite, ideal-gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence-position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of short-range interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 A global root-mean-squared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.     

钝裂银莲花花粉活力测定方法的研究

以3种花色（黄色、浅黄色和白色）钝裂银莲花为研究对象,分别采用TTC染色、I2-I染色、无机酸测定和蔗糖萌发4种方法,测定了钝裂银莲花（Anemone obtusiloba）的花粉活力,同时比较了不种方法对花粉活力的测定效果,并了解了花粉活力在一天内的动态变化情况。结果表明：（1）钝裂银莲花花粉可育率很高,达80%左右。花粉直径为28.75~33.75 m 。（2）TTC浓度影响花粉活力的测定,当浓度为0.5%时,所测花粉活力的效果较好。（3）I2-I法的染色效果不理想,染色率仅为8.33%~22.2%,且3种花色花粉活力测定数据间差异不显著。（4）3种花色钝裂银莲花花粉活力有差异,黄色最高,浅黄色次之,白色最低。TTC染色法是简单快速测定钝裂银莲花花粉活力的最适方法。一天内花粉活力在12:00~14:00最大。     

Complementarity and other key criteria in the conservation of herb-rich forests in Finland

Complementarity of the nature reserve network in southernmost Finlandwas examined using a simple heuristic algorithm and occurrence data of 75characteristic herb-rich forest vascular plant species in 126 protected and 120non-protected sites. Three different minimum sets were selected to represent 1,5, or 10 occurrences of each species. In each minimum set there weresignificantly more protected than non-protected sites. Thus, although efficiencyis not maximal in the existing reserve network, the network does provide arepresentative basis for the conservation of herb-rich forest plants. However,some deficiencies were also noticed, particularly new reserves in floristicallydiverse herb-rich forests along watercourses would supplement the existingreserve network. On the other hand, the growing concern over the shortcomings ofreserve selection studies using presence/absence data is echoed here, becausemany of the protected forests not included in the minimum sets harbour importantnature conservation values. With regard to the five biological reserve selectioncriteria (e.g. occurrences of threatened species) considered here, theperformance of the existing reserve network is rather good. However, examinationof five reserve design criteria revealed some deficiencies, particularlyvulnerability of many reserves to potential edge effects.