Is there a star tree paradox?

Concerns have been raised that posterior probabilities on phylogenetic trees can be unreliable when the true tree is unresolved or has very short internal branches, because existing methods for Bayesian phylogenetic analysis do not explicitly evaluate unresolved trees. Two recent papers have proposed that evaluating only resolved trees results in a "star tree paradox": when the true tree is unresolved or close to it, posterior probabilities were predicted to become increasingly unpredictable as sequence length grows, resulting in inflated confidence in one resolved tree or another and an increasing risk of false-positive inferences. Here we show that this is not the case; existing Bayesian methods do not lead to an inflation of statistical confidence, provided the evolutionary model is correct and uninformative priors are assumed. Posterior probabilities do not become increasingly unpredictable with increasing sequence length, and they exhibit conservative type I error rates, leading to a low rate of false-positive inferences. With infinite data, posterior probabilities give equal support for all resolved trees, and the rate of false inferences falls to zero. We conclude that there is no star tree paradox caused by not sampling unresolved trees.     

A null model of exotic plant diversity tested with exotic and native species-area relationships

At large spatial scales, exotic and native plant diversity exhibit a strong positive relationship. This may occur because exotic and native species respond similarly to processes that influence diversity over large geographical areas. To test this hypothesis, we compared exotic and native species–area relationships within six North American ecoregions. We predicted and found that within ecoregions the ratio of exotic to native species richness remains constant with increasing area. Furthermore, we predicted that areas with more native species than predicted by the species–area relationship would have proportionally more exotics as well. We did find that these exotic and native deviations were highly correlated, but areas that were good (or bad) for native plants were even better (or worse) for exotics. Similar processes appear to influence exotic and native plant diversity but the degree of this influence may differ with site quality.     

Ecological resistance, seed density and their interactions determine patterns of invasion in a California coastal grassland

Relatively little experimental evidence is available regarding how ecological resistance and propagule density interact in their effects on the establishment of invasive exotic species. We examined the independent and interactive effects of neighbour cover (biotic resistance), winter vs. spring water addition (abiotic resistance) and seed density on the invasion of the European perennial grass Holcus lanatus into a California coastal grassland dominated by exotic annual grasses. We found that decreased competition from resident exotic grasses had no effect. In contrast, increased late-season water availability eroded the abiotic resistance offered by naturally dry conditions, facilitating invasion. Finally, watering treatment and seed density interacted strongly in determining seedling survival: while seedling mortality was close to 100% in ambient and winter water addition plots, survivor numbers increased with seed density in spring-watered plots. Thus, decreased abiotic resistance can amplify the effect of increased propagule density on seedling establishment, thereby increasing the likelihood of invasion.     

In other words: external modifiers in Georgian

This paper addresses the issue of stranded modifiers and null heads through two otherwise unrelated constructions in Georgian. In each construction, a word in the oblique form modifies part of the complex word following it. It is shown that null modifiers in Georgian have a form different from that of the modifiers in the constructions at issue, and the latter cannot have null heads. However, Baker’s [Baker, M. C. (1988). Incorporation: A theory of grammatical function changing. Chicago: University of Chicago Press.] alternative approach is not easily compatible with the derivational morphology of these examples. I propose an analysis of external modifiers in terms of Beard [Beard, R. (1991). Natural Language and Linguistic Theory, 9, 195–229.], which addresses other bracketing paradoxes by permitting “the semantic features of an attribute [to] subjoin with one and only one semantic feature of its head” (1991: 208). In this way I suggest a unified analysis of noun incorporation and derived structures, drawing on a mechanism that must be included in the grammar for non-derived words as well.     

Back to Units of Protein Folding

Abstract

In response to the criticism by A. Finkelstein (J. Biomol. Struct. Dyn. 20, 311–314, 2002) of our Communication (J. Biomol. Struct. Dyn. 20, 5–6, 2002) several issues are dealt with. Importance of the notion of elementary folding unit, its size and structure, and the necessity of further characterization of the units for the elucidation of the protein folding in vivo are discussed. The criticism (J. Biomol. Struct. Dyn. 20, 311–314, 2002) on the hierarchical protein folding is also briefly addressed.     

Loop Folds in Proteins and Evolutionary Conservation of Folding Nuclei

Abstract

We show that loops of close contacts involving hydrophobic residues are important in protein folding. Contrary to Berezovsky and Trifonov (J. Biomol. Struct. Dyn. 20, 5–6, 2002) the loops important in protein folding usually are much larger in size than 23–31 residues, being instead comparable to the size of the protein for single domain proteins. Additionally what is important are not single loop contacts, but a highly interconnected network of such loop contacts, which provides extra stability to a protein fold and which leads to their conservation in evolution.     

"蒸发悖论"在秦岭南北地区的探讨

潜在蒸散量(ET0)是大气蒸发的估计值,已经广泛应用于灌溉管理和无实测蒸发资料地区的估算.分析ET0的时空变化是研究水资源对气候变化响应的基础工作,同时对于农业水资源的优化利用也具有重要意义.根据秦岭南北47个气象站1960-2011年逐日数据,利用FAO Penman-Monteith公式计算出各站的潜在蒸散量(ET0),研究了气温、降水与ET0之间的长期变化趋势关系,对导致ET0下降的主要原因进行了讨论,着重对秦岭南北地区是否存在“蒸发悖论”进行验证.结果表明:(1)秦岭南北整体气温经历了先降后升的变化过程,1993年为突变年份,1960-1993年的降温速率和1994-2011年的升温速率均表现出由南向北递减的规律,1960-2011年整体升温速率由北向南递减.(2)1979年和1993年是ET0变化的转折点,以1979和1993为界ET0经历了“升—降—降”的变化阶段.1960-1979年仅汉水流域和巴巫谷地存在“蒸发悖论”现象,1980-1993、1994-2011和1960-2011年3个时段区域整体和各子区均发现了“蒸发悖论”现象.秋季后18a和52a整体以及冬季前34a和52a整体均存在“蒸发悖论”现象,冬季最为明显.(3)近52年整体降水表现出不显著的下降趋势,相较于年尺度,夏季降水与ET0逆向变化趋势更为明显.(4)年尺度上,太阳辐射(日照时数)下降引起的潜热通量减少是造成ET0下降即“蒸发悖论”现象的主要原因.季节尺度,春季ET0下降的主导因素为风速,其它季节均为太阳辐射(日照时数).     

Impacts of extreme climatic events on competition during grassland invasions

Phytometers of five C3 and five C4 species were transplanted into three different grasslands to study the effects of extreme climatic events on community invasibility and competition. Single extreme heating (eight hours at 52.5 °C) and rainfall (the equivalent of 100 mm) events in factorial combinations were superimposed on the grassland communities. A novel technique involving portable computer‐controlled chambers was used to create the heating events. In order to generate predictions of response to the extreme climatic events, the 10 phytometer species were categorized on the basis of 12 key plant functional traits. Using principal component analysis, two functional types (FTs) were identified as most likely to be advantaged (FT1, fast‐growing C4 annuals) and disadvantaged (FT2, slower‐growing C3 perennials) by an extreme climatic event. Competition between the resident vegetation and FT1 plus other C4 phytometers was consistently more intense within the exclusively C3 community compared to the dry C3/C4 community or moist C3/C4 community. The single extreme heating event had the greatest impact on competition, lowering the intensity of competition between the phytometers and resident vegetation. Our results indicate that competition is highly important in limiting the invasion of C3 grasslands by C4 species. The FT1 and FT2 responses confirmed predictions based on plant functional traits, whether growing as phytometers or as part of the resident vegetation. Future increases in climatic variability and the incidence of extreme climatic events are expected to suppress C3 competitive dominance and promote invasion of C4 species, in particular, the FT1 species.     

Native communities determine the identity of exotic invaders even at scales at which communities are unsaturated

Aim To determine why some communities are more invasible than others and how this depends on spatial scale. Our previous work in serpentine ecosystems showed that native and exotic diversity are negatively correlated at small scales, but became positively correlated at larger scales. We hypothesized that this pattern was the result of classic niche partitioning at small scales where the environment is homogeneous, and a shift to the dominance of coexistence mechanisms that depend on spatial heterogeneity in the environment at large scales. Location Serpentine ecosystem, Northern California. Methods We test the above hypotheses using the phylogenetic relatedness of natives and exotics. We hypothesized that (1) at small scales, native and exotic species should be more distantly related than expected from a random assemblage model because with biotic resistance, successful invaders should have niches that are different from those of the natives present and (2) at large scales, native and exotic species should not be more distantly related than expected. Result We find strong support for the first hypothesis providing further evidence of biotic resistance at small scales. However, at large scales, native and exotic species were also more distantly related than expected. Importantly, however, natives and exotics were more distantly related at small scales than they were at large scales, suggesting that in the transition from small to large scales, biotic resistance is relaxed but still present. Communities at large scales were not saturated in the sense that more species could enter the community, increasing species richness. However, species did not invade indiscriminately. Exotic species closely related to species already established the community were excluded. Main conclusions Native communities determine the identity of exotic invaders even at large spatial scales where communities are unsaturated. These results hold promise for predicting which species will invade a community given the species present.     

Effects of land use and environment on alien and native macrophytes: lessons from a large‐scale survey of Australian rivers

Aim We sampled riverine macrophyte communities and environmental conditions to compare drivers of alien and native abundance and to provide a general set of environmental correlates of invasion by aquatic macrophytes. Location Streams adjacent to three land‐use types (intensive, agricultural and natural) across a large latitudinal gradient (approximately 27° S–43° S) in Australia. Sites were located near Brisbane (Queensland), Sydney (New South Wales), Canberra (Australian Capital Territory), Melbourne (Victoria) and Hobart (Tasmania). Methods Alien and native aquatic plant species cover, water quality, forest canopy and adjacent land use were measured in three catchment locations (low‐, mid‐ and upper‐catchment) in all cities. Mean richness and cover of native and alien macrophytes were compared in the five cities, three catchment locations, and three land‐use types. Correlation tests examined relationships between alien and native richness at transect, site and city scales. Canonical correspondence analysis (CCA) determined the effects of environment on cover and richness of native and alien plant groups (emergents, floating, forbs/other, graminoids and submerged). Results Variation existed in the aquatic plant community at all scales, but strong patterns emerged with respect to land use and environmental gradients. Alien abundance was more responsive to anthropogenic disturbance (e.g. greater in intensive and agricultural land‐use types, and greater where dissolved nutrients and conductivity were high) than natives, which were unaffected by land‐use type and less responsive overall to environmental gradients. Native and alien richness were uncorrelated at all scales. Main conclusions Natives and aliens of the same life form did not respond similarly to the environment, suggesting inherent differences in their ability to capitalize on anthropogenic disturbance. Our results suggest invasion‐susceptible habitats are those that receive nutrient pollutants and that occur in urban and agricultural areas low in the catchment. Our confidence in these patterns is strengthened by their consistency across a large latitudinal gradient.