Trees and/or networks to display intraspecific DNA sequence variation?

Phylogenetic trees and networks are both used in the scientific literature to display DNA sequence variation at the intraspecific level. Should we rather use trees or networks? I argue that the process of inferring the most parsimonious genealogical relationships among a set of DNA sequences should be dissociated from the problem of displaying this information in a graph. A network graph is probably more appropriate than a strict consensus tree if many alternative, equally most parsimonious, genealogies are to be included. Within the maximum parsimony framework, current phylogenetic inference and network‐building algorithms are both unable to guarantee the finding of all most parsimonious (MP) connections. In fact, each approach can find MP connections that the other does not. Although it should be possible to improve at least the maximum parsimony approach, current implementations of these algorithms are such that it is advisable to use both approaches to increase the probability of finding all possible MP connections among a set of DNA sequences.     

我国春玉米潜在种植分布区的气候适宜性

根据中国气象局216个春玉米农业气象观测站资料与1971—2000年10 km×10 km空间分辨率的气候资料,基于全国区域和年尺度筛选出了影响我国玉米种植分布的潜在气候指标,利用最大熵(Maximum Entropy,MaxEnt)模型和ArcGIS空间分析技术,构建了春玉米潜在种植分布与气候因子关系模型,研究了影响我国春玉米潜在种植分布区的主导气候因子及其气候适宜性。结果表明,影响我国春玉米潜在种植分布的主导气候因子有:≥10℃积温、≥10℃的天数、最热月平均温度、年平均温度、年降水、湿润指数和气温年较差;结合春玉米存在概率,将我国春玉米潜在种植分布区划分成4个等级:气候不适宜区、次适宜区、适宜区和最适宜区,给出了各气候适宜区的气候特征。选取作物在待预测地区的存在概率这一综合反映各主导气候因子影响的指标来划分作物潜在种植分布区,有助于更加准确地进行气候区划,从而可为制定玉米应对气候变化措施提供科学依据。     

Sphingosylphosphorylcholine induces stress fiber formation via activation of Fyn-RhoA-ROCK signaling pathway in fibroblasts

Sphingosylphosphorylcholine (SPC), a bioactive sphingolipid, has recently been reported to modulate actin cytoskeleton rearrangement. We have previously demonstrated Fyn tyrosine kinase is involved in SPC-induced actin stress fiber formation in fibroblasts. However, Fyn-dependent signaling pathway remains to be elucidated. The present study demonstrates that RhoA-ROCK signaling downstream of Fyn controls stress fiber formation in SPC-treated fibroblasts. Here, we found that SPC-induced stress fiber formation was inhibited by C3 transferase, dominant negative RhoA or ROCK. SPC activated RhoA, which was blocked by pharmacological inhibition of Fyn activity or dominant negative Fyn. Constitutively active Fyn (ca-Fyn) stimulated stress fiber formation and localized with F-actin at the both ends of stress fibers, both of which were prevented by Fyn translocation inhibitor eicosapentaenoic acid (EPA). In contrast, inhibition of ROCK abolished only the formation of stress fibers, without affecting the localization of ca-Fyn. These results allow the identification of the molecular events downstream SPC in stress fiber formation for a better understanding of stress fiber formation involving Fyn.     

亚热带城乡复合系统BVOC排放清单——以台州地区为例

挥发性有机复合物(VOC)对大气的化学组成有重要的影响。植物排放的VOC(BVOC)比人为源VOC(AVOC)具有更高的反应活性。通过实地调查台州地区的植被构成和分布,综合BVOC排放速率的测定值和文献数值、当地气象资料等,研究了台州城市和周边地区的BVOC排放强度、时空格局及种类特征。结果表明,2009年台州地区的BVOC年排放量为4.6×1010 g C,其中异戊二烯、单萜和其他VOC所占的比重分别为93.8%、3.5%和2.7%。野外森林中毛竹林排放强度(133.8 t C.km-.2a-1)高出马尾松林、杉木林和常绿阔叶林(分别为0.9、0.8、0.6 t C.km-.2a-1)2个数量级,因此从改善大气质量角度考虑应当抑制毛竹林的扩张。城市行道树及河道树的BVOC排放强度为2.4 t C.km-.2a-1,公园及居民区绿地为1.6 t C.km-.2a-1,均高于野外除毛竹林外的其他植被类型。台州市区的主要树种中,垂柳、合欢、龙爪槐和枫香的单株排放强度较高,而香樟、广玉兰、银杏等单株排放强度相对较低。可优先选择这些排放强度低的树种用作城市绿化。研究结果也可为处在相近气候带的城市中绿化树种的选择和大气质量的改善提供科学依据。     

北部湾秋季底层鱼类多样性和优势种数量的变动趋势

根据1992年、2001年和2006年秋季在北部湾进行的底拖网调查数据,对该海域鱼类的种类组成、物种多样性、优势种及其数量的变动趋势进行分析。1992年共记录鱼类171种,隶属17目77科;2001年记录鱼类156种,隶属18目71科;2006年记录157种,隶属17目67科。3个年代记录的鱼类均以鲈形目的种类数最多,其中1992年为96种(占56.14%)、2001年90种(占57.69%)和2006年89种(占56.69%)。鱼类的Pielou均匀度指数(J')和Shannon-Wiener多样性指数(H')的变化趋势一致:以2001年最高,为0.72和3.64;其次为1992年,为0.64和3.27;2006年最低,分别为0.52和2.64。丰富度指数(D)呈逐年下降的趋势:为1992年的21.03,2001年的20.74和2006年的19.61。建立非线性回归模型对北部湾3个年代出现的6种共有优势种(发光鲷Acropoma japonicum、带鱼Trichiurus haumela、二长棘鲷Parargyrops edita、黄斑鲾Leiognathus bindus、竹荚鱼Trachurus japonicus和黄带绯鲤Upeneus sulphureus)的数量变化趋势进行分析。结果表明:北部湾鱼类中的经济价值较高的优势种逐渐被低值和小型的鱼类所替代,但繁殖力较强和寿命较短的鱼类变动较小。在6种共同优势种中,黄斑鲾和发光鲷的渔获率呈上升趋势;带鱼和黄带绯鲤的渔获率呈下降趋势;而二长棘鲷和竹荚鱼的渔获率基本保持不变。研究结果表明,北部湾鱼类的优势种更替明显,总体变化趋势是k选择种类(以红笛鲷和黑印真鲨等为代表)逐渐被r选择种类(发光鲷、鲾科和天竺鱼科等为代表)所替代,即寿命长、个体大和营养级高的鱼类数量减少,寿命短、个体小和营养级较低的种类增多。     

Crystal structure and characterization of coiled-coil domain of the transient receptor potential channel PKD2L1

The cation-permeable channel PKD2L1 forms a homomeric assembly as well as heteromeric associations with both PKD1 and PKD1L3, with the cytoplasmic regulatory domain (CRD) of PKD2L1 often playing a role in assembly and/or function. Our previous work indicated that the isolated PKD2L1 CRD assembles as a trimer in a manner dependent on the presence of a proposed oligomerization domain. Herein we describe the 2.7 Å crystal structure of a segment containing the PKD2L1 oligomerization domain which indicates that trimerization is driven by the β-branched residues at the first and fourth positions of a heptad repeat (commonly referred to as “a” and “d”) and by a conserved R-h-x-x-h-E salt bridge motif that is largely unique to parallel trimeric coiled coils. Further analysis of the PKD2L1 CRD indicates that trimeric association is sufficiently strong that no other species are present in solution in an analytical ultracentrifugation experiment at the lowest measurable concentration of 750 nM. Conversely, mutation of the “a” and “d” residues leads to formation of an exclusively monomeric species, independent of concentration. Although both monomeric and WT CRDs are stable in solution and bind calcium with 0.9 μM affinity, circular dichroism studies reveal that the monomer loses 25% more α-helical content than WT when stripped of this ligand, suggesting that the CRD structure is stabilized by trimerization in the ligand-free state. This stability could play a role in the function of the full-length complex, indicating that trimerization may be important for both homo- and possibly heteromeric assemblies of PKD2L1.     

Predictable changes in aboveground allometry of trees along gradients of temperature,aridity and competition

Aim Trees are often observed to get shorter and more narrowly crowned in dry regions and at high elevations. We explore how this pattern is driven by two opposing factors: competition for light makes it advantageous to extend branches to their biomechanical limit, whereas under cold or arid conditions it is advantageous to have shorter branches, thereby reducing the length of the hydraulic transport system and embolism risk. Using data from 700,000 trees of 26 species, we quantify how environmental conditions influence the scaling of height and crown diameter (CD) with stem diameter (d.b.h.). We compare our predictions with those of metabolic scaling theory (MST), which suggests that allometry is invariant of environment. Location 48,000 inventory plots that systematically sample mainland Spain, a region in which climate varies strongly. Methods We fit d.b.h.–height and d.b.h.–CD functions using Bayesian methods, allowing comparison of within‐ and across‐species trends in allometry along gradients of temperature, precipitation, drought and competition for light (i.e. the basal area of taller trees). Results The competitive environment had a strong influence on aboveground allometry, but all trees were far shorter than predicted by biomechanical models, suggesting that factors other than biomechanics are important. Species that dominate in arid and cold habitats were much shorter (for a given diameter) than those from benign conditions; but within‐species heights did not vary strongly across climatic gradients. Main conclusions Our results do not support the MST prediction that d.b.h.–height and d.b.h.–CD allometries are invariant, or that biomechanical constraints determine height allometry. Rather, we highlight the role of hydraulic limitations in this region. The fact that intra‐specific adjustment in d.b.h.–CD – height allometry along environmental gradients was far weaker than across‐species changes may indicate genetic constraints on allometry which might contribute to niche differentiation among species.     

Patterns of woody plant invasion in an Argentinean coastal grassland

Coastal dune grasslands are fragile ecosystems that have historically been subjected to various types of uses and human activities. In Buenos Aires Province (Argentina), these areas are frequently afforested for urban and touristic development. The introduction and subsequent spread of exotic tree species is one of the main threats to conservation of natural grasslands as invasive trees strongly transform their structure and composition. The aim of this study was to identify patterns of woody plant invasion comparing plant communities and environmental variables between invaded and non-invaded areas surrounding the coastal village of Mar Azul, Argentina. Coastal grasslands in this area are being invaded by Populus alba (white poplar) and Acacia longifolia (coast wattle). The height of the saplings and the richness of the accompanying vegetation were evaluated in relation to the distance from the edge of the mature tree patches. Also, the cover, richness and diversity of all species in the invaded and non-invaded areas were measured, as well as soil pH, temperature and particle size. Negative correlations were found between the height of the saplings and distance to mature tree patches in all areas. The richness of the accompanying vegetation was negatively and positively correlated with the distance from the poplar and acacia area, respectively. The most abundant native species was Cortaderia selloana. Less cover, richness and diversity of native plant species and greater soil particle size were found in invaded areas, where the proportion of bare soil was higher. Also, a higher proportion of leaf litter in the invaded areas was registered. The results emphasize the invasive capacity of P. alba and A. longifolia advancing on the native communities and reducing their richness. Knowledge of the impact of invasive woody plants in coastal grasslands is important to design active management strategies for conservation purposes.     

Bioaccumulation and biochemical response in South American native species exposed to zinc: Boosted regression trees as novel tool for biomarkers selection

The aim of this study was to evaluate the response of a wide battery of biomarkers in two native species, the freshwater shrimp Palaemonetes argentinus and the macrophyte Potamogeton pusillus, experimentally exposed to zinc in order to establish the potential use of selected species as bioindicators of aquatic pollution. For this purpose, we propose the use of integrated biomarker index (IBR) with a previous selection of biomarkers using boosted regression trees (BRTs) as a new tool in ecotoxicology. Organisms were collected from a reference site, acclimated and exposed at relevant environmental zinc levels (control, 5, 50 and 500 μg Zn L⁻¹) for 96 h. Biomarkers were measured in cephalothorax and abdomen of shrimp as well as in leaf, stem and root of plants.Significant zinc accumulation was observed in cephalothorax of P. argentinus from 50 μg Zn L⁻¹ and from 5 μg Zn L⁻¹ in stem and root of P. pusillus, when compared with control condition. Those effect biomarkers with significant differences among treatments were pre-selected to run out the BRTs model for each species. In P. argentinus, microsomal acetylcholinesterase activity, metallothioneins and superoxide dismutase activity measured in cephalothorax, as well as glutathione reductase activity in abdomen, showed the higher capacity to explain or predict the zinc exposure concentration. On the contrary, in P. pusillus, only chlorophyll a measured in leaf and H₂O₂ measured in root were the more representative of exposure concentrations, at least, within the biomarkers tested in the present study. Thereafter, IBR was calculated with the selected biomarkers in P. argentinus and showed in a sole value the organism stress, which also correlates with zinc exposure and accumulation.Natives species tested displayed a sensitive response to metal exposure, which represents an important characteristic for biomonitoring programs. Our findings suggest that the BRTs and IBR are useful and robust run tools to select the better biomarkers in toxicological studies and indicate the organism stress.     

Decline in local ecological knowledge in the Colombian Andes may constrain silvopastoral tree diversity

Local ecological knowledge (LEK) can play an important role in ecological restoration by guiding landholder decision‐making towards more ecologically oriented land management. Silvopastures are a promising option for restoring ecological function to degraded landscapes because they increase tree cover and diversity, moderating the impacts of cattle production on ecological processes. Some silvopastoralists possess considerable LEK that can shape silvopastoral tree communities, but little is known about the temporal trends of this knowledge base. We followed up on a survey of workers, managers, and owners of silvopastoral farms in the Colombian Andes 6 years later and found that the ability to identify native trees and describe their uses, and interest in tree planting, were significantly lower. Importantly, the likelihood that an individual would plant a species was linked directly to the number of uses they listed for that species. Furthermore, the utility of species became more important for influencing the probability of planting native trees over time, as general interest in planting trees declined. We show that knowledge about the uses of native trees is critical for promoting cultivation of diverse tree species in silvopastoral systems, and that multipurpose trees are most likely to be planted. Moreover, our results suggest that the socio‐economic changes driving declines in ecological knowledge elsewhere, including outmigration and limited transmission of knowledge to younger generations, appear to erode LEK among Colombian silvopastoralists. Preserving LEK is therefore a critical factor for ensuring silvopastoral and other agro‐ecosystems can contribute to efforts to restore ecological integrity to degraded landscapes.