Integrating sample similarities into latent class analysis: a tree-structured shrinkage approach

This paper is concerned with using multivariate binary observations to estimate the probabilities of unobserved classes with scientific meanings. We focus on the setting where additional information about sample similarities is available and represented by a rooted weighted tree. Every leaf in the given tree contains multiple samples. Shorter distances over the tree between the leaves indicate a priori higher similarity in class probability vectors. We propose a novel data integrative extension to classical latent class models with tree-structured shrinkage. The proposed approach enables (1) borrowing of information across leaves, (2) estimating data-driven leaf groups with distinct vectors of class probabilities, and (3) individual-level probabilistic class assignment given the observed multivariate binary measurements. We derive and implement a scalable posterior inference algorithm in a variational Bayes framework. Extensive simulations show more accurate estimation of class probabilities than alternatives that suboptimally use the additional sample similarity information. A zoonotic infectious disease application is used to illustrate the proposed approach. The paper concludes by a brief discussion on model limitations and extensions.     

Osteological and histological comparison of the development of the interphalangeal intercalary skeletal element between hyloid and ranoid anurans

Some frog species have a unique skeletal element, referred to as the intercalary element (IE), in the joints between the terminal and subterminal phalanges of all digits. IEs are composed of cartilage or connective tissue and have a markedly differ shape than the phalanges. IEs are highly related to the arboreal lifestyle and toe pads. The IE is found only in neobatrachian frogs among anurans, suggesting that it is a novelty of Neobatrachia. IEs are widely distributed among multiple neobatrachian lineages and are found in the suborders Hyloides and Ranoides (the two major clades in Neobatrachia). However, it is unclear whether the IEs found in multiple linages resulted from convergent evolution. Therefore, in this study, we aimed to examine how similar or different the developmental trajectories of the IEs are between Hyloides and Ranoides. To that end, we compared the osteological and histological developmental processes of the IEs of the hyloid frog Dryophytes japonicus and the ranoid frog Zhangixalus schlegelii. Both species shared the same IE-initiation site and level of tissue differentiation around the IE when it began to form in tadpoles, although the IE developments initiated at different stages which were determined by external criteria. These results suggest that similar mechanisms drive IE formation in the digits of both species, supporting the hypothesis that the IEs did not evolve convergently.     

Canopy tree mortality depends on the proportion of crown exposed to sunlight,but this effect varies with species' wood density

Understanding what drives changes in tree mortality as well as the covariates influencing trees' response is a research priority to predict forest responses to global change. Here, we combined drone photogrammetry and ground-based data to assess the influence of crown exposure to light (relative to total crown area), growth deviations (relative to conspecifics), tree size, and species' wood density (as a surrogate for light-demanding and shade-tolerant life-history strategies) on the mortality of 984 canopy trees in an Amazon terra firme forest. Trees with lower wood density were less prone to die when their proportion of crown was more exposed to sunlight, but this relationship with relative crown exposure weakened and slightly reversed as wood density increased. Trees growing less than their species average had higher mortality, especially when the species' wood density decreased. The role of wood density in determining the survival of canopy trees under varying light conditions indicates differential responses of light-demanding versus shade-tolerant species. Our results highlight the importance of accounting for life-history strategies, via plant functional types, in vegetation dynamic models aiming to predict forest demography under a rapidly changing climate. Abstract in Spanish is available with online material.     

陕西省野生拟黑虫草的多基因分子生物学鉴定

虫草是中国重要的生物资源,为明确从陕西省旬邑县石门山林区采集到的1种野生虫草种类及其虫生真菌(虫草菌DY6F)的分类地位,研究在利用PCR技术对该虫草子实体的核糖体内转录间隔区(internal transcribed spacer, ITS)、延伸因子1α(elongation factor 1α,EF-1α)和RNA聚合酶Ⅱ大亚基(RNA polymeraseⅡlarge subunit, RPB1)的基因片段进行扩增与测序的基础上,分别基于这3个基因片段构建单基因系统进化树,并基于EF-1α和RPB1 2个基因联合序列构建多基因系统进化树。结果显示,该虫草子实体的这些基因序列与线虫草属拟黑虫草菌(Ophiocordyceps nigrella)的相应基因序列相似度为99%～100%,且在进化树上,二者聚于同一分支,支持率均为100%。因此,虫草菌DY6F被鉴定为拟黑虫草菌,该虫草为拟黑虫草。     

茶树品种‘金牡丹’自然杂交后代遗传鉴定

为了对‘金牡丹’茶树自然杂交后代进行遗传鉴定,利用EST-SSR毛细管电泳荧光标记技术对65个金牡丹自然杂交后代进行研究。结果表明,28对SSR标记共扩增出192个等位片段,平均等位基因数(Na)、平均观测杂合度(Ho)及遗传多态信息量(PIC)分别为6.86、0.540、0.532。单亲基因型已知时的累积排除概率为0.999,说明选择的28对SSR标记位点具有高度的多态性和较高的排除概率,适用于遗传分析和个体的亲子鉴定。15个‘金牡丹’自然杂交后代的遗传鉴定结果表明,MD44、JMD45、JMD47、JMD32为早生绿茶类型;JMD51、JMD53为闽北肉桂乌龙茶类型;MD2、JMD56为闽南‘铁观音’乌龙茶类型;JMD24、JMD26、JMD29、JMD55、JMD59、JMD27、JMD61为‘黄棪’乌龙茶类型。     

Behavioural responses of the vine weevil, Otiorhynchus sulcatus, to semiochemicals from conspecifics, Otiorhynchus salicicola, and host plants

The vine weevil Otiorhynchus sulcatus is a parthenogenetic reproducing species which forages for suitable host plants at night, but is found congregated in dark places during the day. Frass of this weevil species is suspected to contain attractive compounds that are host‐plant related. Using a still‐air olfactometer, we tested adult vine weevils at night for their behavioural response to odours from conspecifics, feeding on a mixture of spindle tree (Euonymus fortunei) and yew (Taxus baccata), and to a sexually reproducing related species (Otiorhynchus salicicola), feeding on a mixture of ivy (Hedera helix) and cherry laurel (Prunus laurocerasus). Their attraction to conspecifics and O. salicicola appeared to be related to frass production. Freshly collected frass from O. sulcatus and from O. salicicola males and females was attractive. Prunus laurocerasus and H. helix have not been observed to be hosts of the vine weevil in the field. However, our tests showed that the vine weevil was attracted to mechanically damaged leaves of both plant species, whereas undamaged leaves were not attractive. Only undamaged young unfolding leaves of H. helix were also attractive. The attraction to odours from mechanically damaged host and non‐host plants suggested the involvement of compounds that are commonly found in many plant species. The involvement of plant compounds and/or aggregation pheromones in attraction to frass of the vine weevil and frass of the related weevil species O. salicicola is discussed.     

Predation impact of Leptodora kindtii on population dynamics and morphology of Bosmina fatalis and B. longirostris in mesocosms

1. We assessed the impact of predation by the invertebrate predator Leptodora kindtii on Bosmina longirostris and B. fatalis, which show seasonal and reciprocal succession patterns in Lake Suwa, in a mesocosm experiment using 20‐L tanks with or without the predator under different food conditions. We also analysed morphological responses of the two Bosmina species to the predator in the tanks. 2. Bosmina fatalis dominated B. longirostris regardless of predator presence under high food density. However, the presence of Leptodora induced the dominance of B. fatalis more rapidly than its absence. On the contrary, no dominance of B. fatalis was observed in tanks with low food density, irrespective of the presence of the predator. Only B. fatalis showed morphological changes in response to the presence of Leptodora. 3. Mucrone length and antennule shape (angle between body and antennule and angle between antennules) showed marked responses at both high and low food densities, but antennule length responded only at high food density. Mucrone length seems to be a more effective defence against Leptodora. 4. The results suggest that B. fatalis is a superior competitor against B. longirostris and is more resistant to Leptodora predation, especially in good food conditions. The repeatedly observed seasonal succession of the two Bosmina species in the eutrophic Lake Suwa – the replacement of B. longirostris by B. fatalis following the occurrence of abundant Leptodora– seems to be caused by the selective predation of Leptodora on B. longirostris as well as the competitive ability of B. fatalis.     

Impact and management of the eriophyoid mite Trisetacus juniperinus on the evergreen cypress Cupressus sempervirens

Abstract 1 In the Mediterranean region, the eriophyoid mite Trisetacus juniperinus causes considerable damage to the evergreen cypress, Cupressus sempervirens L., particularly in nurseries and young stands, disturbing the apical growth of the tree. 2 The impact of mites on survival and apical growth of two commercial clones of cypress (Agrimed and Bolgheri), as well as the results of differently timed pesticide applications to suppress mite population on newly grafted trees, were evaluated. 3 Mites easily infested clonal scions from rootstocks that were previously infested in the nursery, inducing tip deformation and disturbance of the growth. Apical growth was significantly lower in infested than in control trees 2 years following the graft. 4 Deformed apical buds were left early by mites, which dispersed in the crown and may have incurred high mortality. This is interpreted as a defensive reaction of the cypress to the mite attack, which involves costs resulting in reduced apical growth in both clones. However, mites partly overcame tree defences in the Bolgheri clone. 5 Healthy rootstock and graft material should be used to limit damage and maintain plant growth because natural infestations rarely occur. In case of attack, a pesticide should be applied as soon as possible because precocious mite infestation has a log‐lasting effect on tree growth, with considerable economic damage.     

Soil-surface carbon dioxide efflux and microbial biomass in relation to tree density 13 years after a stand replacing fire in a lodgepole pine ecosystem

The effects of fire on soil‐surface carbon dioxide (CO₂) efflux, F_S, and microbial biomass carbon, C_mic, were studied in a wildland setting by examining 13‐year‐old postfire stands of lodgepole pine differing in tree density (< 500 to > 500 000 trees ha^?1) in Yellowstone National Park (YNP). In addition, young stands were compared to mature lodgepole pine stands (～110‐year‐old) in order to estimate ecosystem recovery 13 years after a stand replacing fire. Growing season F_S increased with tree density in young stands (1.0 µmol CO₂ m^?2 s^?1 in low‐density stands, 1.8 µmol CO₂ m^?2 s^?1 in moderate‐density stands and 2.1 µmol CO₂ m^?2 s^?1 in high‐density stands) and with stand age (2.7 µmol CO₂ m^?2 s^?1 in mature stands). Microbial biomass carbon in young stands did not differ with tree density and ranged from 0.2 to 0.5 mg C g^?1 dry soil over the growing season; C_mic was significantly greater in mature stands (0.5–0.8 mg C g^?1 dry soil). Soil‐surface CO₂ efflux in young stands was correlated with biotic variables (above‐ground, below‐ground and microbial biomass), but not with abiotic variables (litter and mineral soil C and N content, bulk density and soil texture). Microbial biomass carbon was correlated with below‐ground plant biomass and not with soil carbon and nitrogen, indicating that plant activity controls not only root respiration, but C_mic pools and overall F_S rates as well. These findings support recent studies that have demonstrated the prevailing importance of plants in controlling rates of F_S and suggest that decomposition of older, recalcitrant soil C pools in this ecosystem is relatively unimportant 13 years after a stand replacing fire. Our results also indicate that realistic predictions and modeling of terrestrial C cycling must account for the variability in tree density and stand age that exists across the landscape as a result of natural disturbances.