Internal consistency as a method to assess the quality of dating estimates using multiple markers

Multiple tools are available to infer time in phylogentic reconstructions and multiple markers/genes are generally used to obtain more solid reconstructions, opening to the issue of which marker performs better in dating. Following the observation that multiple markers, applied to the same group of taxa or even to the same topology, generally produce different time estimates, we suggest two new estimators: DD_jk to quantify the discordance between two ultrametric dated trees with identical topology and ID_j to quantify the discordance of one tree with respect to a study-set of trees in terms of their date estimates. Furthermore we suggest a procedure based on a stepwise exclusion algorithm to rank trees from the most to the least consistent with the study-set of trees based on their time estimates. We name the quality of a tree of having time estimates that agree with the majority of other trees as ‘internal consistency’. We applied this procedure to assess the internal consistency of trees individually obtained from 14 mitochondrial markers in 5 insect orders and to test whether one or more markers repeatedly produce dates that are more consistent. Three genes (nad4, nad5 and cytb) repeatedly perform better than others, one (cox2) worse. We suggest this method could be applied in evaluating the performance of different markers preliminary to a dating analysis.     

Monkey electrophysiological and human psychophysical responses to mutants of the sweet protein brazzein: delineating brazzein sweetness

Responses to brazzein, 25 brazzein mutants and two forms of monellin were studied in two types of experiments: electrophysiological recordings from chorda tympani S fibers of the rhesus monkey, Macaca mulatta, and psychophysical experiments. We found that different mutations at position 29 (changing Asp29 to Ala, Lys or Asn) made the molecule significantly sweeter than brazzein, while mutations at positions 30 or 33 (Lys30Asp or Arg33Ala) removed all sweetness. The same pattern occurred again at the beta-turn region, where Glu41Lys gave the highest sweetness score among the mutants tested, whereas a mutation two residues distant (Arg43Ala) abolished the sweetness. The effects of charge and side chain size were examined at two locations, namely positions 29 and 36. The findings indicate that charge is important for eliciting sweetness, whereas the length of the side-chain plays a lesser role. We also found that the N- and C-termini are important for the sweetness of brazzein. The close correlation (r = 0.78) between the results of the above two methods corroborates our hypothesis that S fibers convey sweet taste in primates.     

Discounting of sequences of delayed rewards of different amounts

The main purpose of this study was to determine whether the magnitude effect is present in cases where delayed sequences of rewards are discounted. The magnitude effect refers to the inverse relationship between the amount of a reward and the steepness of temporal discounting. This study was conducted with a computer program to estimate the indifference points, which served as indicators of the present subjective value of delayed sequences of small and large rewards. In the indifference point the subjective value of a single, immediate reward was equal to the subjective value of the delayed sequence (or to the value of a single delayed reward). As a control condition, we added an experimental task involving choices between single immediate and single delayed rewards. The experiment showed that the sequences of large rewards are discounted less steeply than are the sequences of small rewards. This finding suggests that the magnitude effect is present within the delayed sequences of rewards. In addition, when outcomes are relatively large, the results suggest that a single reward is discounted less steeply than the sequence of a total nominal value equal to this single reward. However, for relatively small rewards, the difference is not statistically significant. The less steep discounting of sequences of large rewards may explain the reward-bundling effect, which refers to less steep discounting of longer sequences than of shorter ones: longer sequences usually have greater overall nominal value. The present study was conducted on hypothetical rewards, and the results should be validated using real rewards.     

Differences between the tactile sensitivity on the anterior torso of normal individuals and those having suffered complete transection of the spinal cord

Using the method of limits and a magnitude estimation procedure, the sense of touch was examined at multiple sites on the anterior torso of normal subjects. Their performance was compared with the performance of individuals having experienced a functionally complete spinal cord transection more than 6 months prior to the tests. Near the insentient regions of the spinal cord-injured patients there was a zone wherein the threshold for light touch was elevated and variable. Within this same transition zone, estimates of the magnitude of a brushing stimulus increased as a linear function of distance from the border for approximately 12 cm away from insentient skin. Throughout the rest of the thorax, spinal cord-injured patients displayed touch thresholds 67% higher than normals and, at the same test sites, spinal cord-injured patients offered estimates of the intensity of the brushing stimulus that averaged 62% higher than normal subjects. The greater intensity of the sensations experienced by spinal cord-injured patients with even very weak stimuli and the smaller range within which they were able to scale stimulus intensity, produced a situation wherein the patients made frequent errors of judgement even on skin regions far from the body parts affected by the lesion. These observations support the hypothesis that spinal cord lesions interrupt tonic modulatory mechanisms having global influences on the sense of touch. This loss produces an elevation of the touch threshold and a reduction of the normal dynamic range of tactile sensory perception for all skin surfaces on the anterior torso.     

The effect of irrigation regimes on plum (Prunus cerasifera) root system development dynamics

Prunus genus species are widely spread in semi-arid regions due to their ability to adjust to the limited water supply. Former research described the effect of water deficit on their aboveground development. However, less is known about the effects of water stress on the development of the root system. In order to investigate the effects of the irrigation regime on the root system development, young plum (Prunus cerasifera) trees were grown under three irrigation regimes for a period of five months. The effects of the irrigation regime on different root order and total root system elongation, biomass growth and tip numbers were analyzed. The results indicate that the responses vary according to the stress level. Under moderate stress, the total root system biomass decreases relative to the full irrigation treatment. However, low-order root formation remains similar to that found under no stress conditions. Under severe stress, the formation of low-order roots is also inhibited. Our results suggest that plum trees’ response to water deficit stress escalates according to the stress level. Namely, moderate stress affects the growth rate of the root system but does not alter the relative contribution of different orders, while severe stress both inhibits the total growth and changes the relative contribution of the different root orders. The combined measurements of the total root system and the different orders enable the identification of a stepwise response to water stress.     

种子重量与海拔的相关性分析

种子重量与海拔的关系是植物生态学中重要而尚存争议的问题。本文对中国123科853种2879份野生植物种子的重量在海拔上的变化特点以及二者之间的相互关系进行了深入研究,结果显示：种子重量总体上与海拔呈负相关,种子重量级别多样性和生活型多样性随海拔上升呈阶梯状下降。但7级种子中,只有100级种子的重量与海拔呈负相关;7种生活型中,只有灌木和匍匐草本的种子重量与海拔呈负相关;在种水平上,只有82%的物种种子重量与海拔存在相关性。本研究揭示了我国种子重量与海拔之间的复杂关系,以及遗传和环境对种子重量的影响,对植物育种、森林管理以及入侵植物的防治具有一定指导意义。     

The effects of heat-induced pain on the detectability,discriminability, and sensation magnitude of vibrotactile stimuli

The effects of heat-induced pain on absolute thresholds, sensation magnitudes and amplitude-difference thresholds were measured at 10 and 100 Hz. Consistent with previous results, heat-induced pain elevated the absolute thresholds by approximately 8.0 dB and lessened the magnitudes of tactile sensations during pain as compared to the non-painful condition. In contrast to these effects, the discriminability of change in the intensity of the vibrotactile stimuli was unaffected by the presence of pain indicating that the effect of pain on tactile sensations is more likely due to sensory rather than cognitive processes (i.e., attention) and that the mechanisms underlying tactile sensitivity as compared to discriminability are different.     

Natural vegetation cover in the landscape and edge effects: differential responses of insect orders in a fragmented forest

Human activities have led to global simplification of ecosystems, among which Neotropical dry forests are some of the most threatened. Habitat loss as well as edge effects may affect insect communities. Here, we analyzed insects sampled with pan traps in 9 landscapes (at 5 scales, in 100–500 m diameter circles) comprising cultivated fields and Chaco Serrano forests, at overall community and taxonomic order level. In total 7043 specimens and 456 species of hexapods were captured, with abundance and richness being directly related to forest cover at 500 m and higher at edges in comparison with forest interior. Community composition also varied with forest cover and edge/interior location. Different responses were detected among the 8 dominant orders. Collembola, Hemiptera, and Orthoptera richness and/or abundance were positively related to forest cover at the larger scale, while Thysanoptera abundance increased with forest cover only at the edge. Hymenoptera abundance and richness were negatively related to forest cover at 100 m. Coleoptera, Diptera, and Hymenoptera were more diverse and abundant at the forest edge. The generally negative influence of forest loss on insect communities could have functional consequences for both natural and cultivated systems, and highlights the relevance of forest conservation. Higher diversity at the edges could result from the simultaneous presence of forest and matrix species, although “resource mapping” might be involved for orders that were richer and more abundant at edges. Adjacent crops could benefit from forest proximity since natural enemies and pollinators are well represented in the orders showing positive edge effects.     

Conservation categories of siluroid fishes in North-East Sundarbans,India

In stock fishery of North-East Sundarbans, siluroid fishes hold a remarkable position owing to the culture potentiality of many of them. Scales in fishes play significant role in protection and resistance against environmental stresses and the lack of scalation in case of siluroid fishes is supposed to be one of the reasons for their decline in eco-degraded aquatic habitats. 11 species of fishes belonging to 9 genera, 8 families under the order Siluriformes have been recorded from different water bodies of North-East Sundarbans, India. Fish Magnitude Value (FMV) of those catfishes were recorded especially by information harvested from local fishermen community and stakeholders as well as from market survey on fish landing. The extensive damage to the population of catfishes in the area has placed the fishes under threat categories. Following the IUCN guidelines and also through Participatory Rural Appraisal (PRA) methods, an attempt has been made to assess the status of such fishes. Trend analysis, Fish Magnitude Value (FMV) and Rank Based Quotient (RBQ) revealed 1 catfish as Endangered, 5 as Vulnerable and 5 as Near Threatened species. The situation warrants immediate attention of ecologists, administrators, managers and entrepreneurs to propose remedial measures for revival of the fishes. The study also delineates distribution, present status and conservation measures for revival of the fishes in North-East Sundarbans wet-land environment of West Bengal, India.