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1.
    
Understanding and predicting the effect of global change phenomena on biodiversity is challenging given that biodiversity data are highly multivariate, containing information from tens to hundreds of species in any given location and time. The Latent Dirichlet Allocation (LDA) model has been recently proposed to decompose biodiversity data into latent communities. While LDA is a very useful exploratory tool and overcomes several limitations of earlier methods, it has limited inferential and predictive skill given that covariates cannot be included in the model. We introduce a modified LDA model (called LDAcov) which allows the incorporation of covariates, enabling inference on the drivers of change of latent communities, spatial interpolation of results, and prediction based on future environmental change scenarios. We show with simulated data that our approach to fitting LDAcov is able to estimate well the number of groups and all model parameters. We illustrate LDAcov using data from two experimental studies on the long‐term effects of fire on southeastern Amazonian forests in Brazil. Our results reveal that repeated fires can have a strong impact on plant assemblages, particularly if fuel is allowed to build up between consecutive fires. The effect of fire is exacerbated as distance to the edge of the forest decreases, with small‐sized species and species with thin bark being impacted the most. These results highlight the compounding impacts of multiple fire events and fragmentation, a scenario commonly found across the southern edge of Amazon. We believe that LDAcov will be of wide interest to scientists studying the effect of global change phenomena on biodiversity using high‐dimensional datasets. Thus, we developed the R package LDAcov to enable the straightforward use of this model.  相似文献   

2.
李其斌  张春雨  赵秀海 《生态学报》2022,42(17):7147-7155
基于长白山3个5.2hm2针阔混交林永久监测样地的野外调查数据,以胸径(DBH)≥1cm的乔木树种为对象,运用R4.0.3软件计算物种多样性指数以及进行物种多样性相关性分析和多元回归分析,以探讨生物和非生物因素对不同演替阶段针阔混交林物种多样性的影响。结果表明:(1)3个典型针阔混交林的4个物种多样性指数均随演替的正向进行而下降,其中物种丰富度、Shannon-Wiener指数和Simpson指数在3个演替阶段存在显著性差异,而Pielou均匀度指数在次生杨桦林与次生针阔混交林阶段差异不显著。(2)胸径结构变量是影响物种多样性变化的主要驱动因子,随着演替的进行,林分密度对物种多样性产生的影响越来越大。(3)所有土壤因子在针阔混交林阶段对物种多样性指数均表现出显著的影响,而在次生杨桦林只有土壤全氮与物种多样性指数存在显著相关关系,土壤全磷在原始椴树红松林阶段是影响物种多样性的主要因素。综上,研究认为在各演替阶段,生物和非生物因素均影响着森林群落的物种多样性,胸径结构和林分密度是影响群落物种多样性的主要因素,林分中的土壤因子受到不同群落特征的影响产生不同变化,从而对群落的物种多样性产生影响也有所不同。  相似文献   

3.
    
A total of 134 bird species were recorded at Jianfengling, Hainan Island, in China from May 2000 to September 2004, of which 44 participated in one or more of 134 mixed‐species flocks. These flocks averaged 3.8 ± 0.2 species and 20.3 ± 1.2 individuals. Flocking propensity in a given species ranged from 1.5 to 100%. For flocking species, frequency of flocking and number of individuals in flocks was positively correlated with frequency and number in point counts. Among all species pairs with flocking frequency above 5%, cluster and correlation analysis indicated there were two principal groups of flocking birds – canopy species and understorey species: associations were positive within a group, but negative between groups. Canopy birds had a higher flocking propensity than understorey birds. They also made significantly less use of inner branches and trunks and greater use of middle branches, and foraged at a significantly greater height when in mixed‐species flocks than when solitary. For understorey bird species, there were no significant differences in foraging locations between solitary and mixed‐species flocks. Higher flocking frequency occurred in the wet season for canopy birds, but in the dry season for understorey birds. Overall patterns were consistent with the explanation that flocking enables an expansion of foraging niche by reducing the risk of predation.  相似文献   

4.
    
The utility of elevational gradients as tools to test either ecological hypotheses and delineate elevation‐associated environmental factors that explain the species diversity patterns is critical for moss species conservation. We examined the elevational patterns of species richness and evaluated the effects of spatial and environmental factors on moss species predicted a priori by alternative hypotheses, including mid‐domain effect (MDE), habitat complexity, energy, and environment proposed to explain the variation of diversity. Last, we assessed the contribution of elevation toward explaining the heterogeneity among sampling sites. We observed the hump‐shaped distribution pattern of species richness along elevational gradient. The MDE and the habitat complexity hypothesis were supported with MDE being the primary driver for richness patterns, whereas little support was found for the energy and the environmental factors.  相似文献   

5.
    
In their recent commentary in Protein Science, Jaskolski et al. analyzed three randomly picked diffraction data sets from fragment‐screening group depositions from the PDB and, based on that, they claimed that such data are principally problematic. We demonstrate here that if such data are treated properly, none of the proclaimed criticisms persist.  相似文献   

6.
    
Each year, millions of hatchery‐reared sea‐run brown trout Salmo trutta L. (the sea trout) juveniles are released into the natural environment in the Atlantic region. The aim of this work was to investigate the growth responses of sea trout to changing temperature conditions and to compare the growth plasticity between wild and hatchery‐reared fish. Scales were collected from sea trout in a selected river flowing into the southern Baltic Sea. We analyzed the scale increment widths as a proxy of somatic growth and investigated the interannual variabilities and differences in growth between fish groups (wild and hatchery‐reared). We used mixed‐effects Bayesian modeling and ascribed the variances in growth to different sources. Furthermore, we developed indices of interannual (2003–2015) growth variation in the marine and freshwater phases of the life cycle of the fish and analyzed the relationships between trout growth and temperature. Temperature positively affects fish growth, regardless of the origin of the fish. We observed stronger relationships between fish growth and temperature conditions in the marine phase than in the freshwater phase. Additionally, wild sea trout are characterized by stronger responses to temperature variability and higher phenotypic plasticity of growth than those of the hatchery‐reared individuals. Therefore, wild sea trout might be better suited to changing environmental conditions than hatchery‐reared sea trout. This knowledge identifies possible threats in management actions for sea trout with an emphasis on ongoing climate change.  相似文献   

7.
    
Most Central African rainforests are characterized by a remarkable abundance of light‐demanding canopy species: long‐lived pioneers (LLP) and non‐pioneer light demanders (NPLD). A popular explanation is that these forests are still recovering from intense slash‐and‐burn farming activities, which abruptly ended in the 19th century. This “human disturbance” hypothesis has never been tested against spatial distribution patterns of these light demanders. Here, we focus on the 28 most abundant LLP and NPLD from 250 one‐ha plots distributed along eight parallel transects (~50 km) in the Yangambi forest. Four species of short‐lived pioneers (SLP) and a single abundant shade‐tolerant species (Gilbertiodendron dewevrei) were used as reference because they are known to be strongly aggregated in recently disturbed patches (SLP) or along watercourses (G. dewevrei). Results show that SLP species are strongly aggregated with clear spatial autocorrelation of their diameter. This confirms that they colonized the patch following a one‐time disturbance event. In contrast, LLP and NPLD species have random or weakly aggregated distribution, mostly without spatial autocorrelation of their diameter. This does not unambiguously confirm the “human disturbance” hypothesis. Alternatively, their abundance might be explained by their deciduousness, which gave them a competitive advantage during long‐term drying of the late Holocene. Additionally, a canonical correspondence analysis showed that the observed LLP and NPLD distributions are not explained by environmental variables, strongly contrasting with the results for the reference species G. dewevrei, which is clearly aggregated along watercourses. We conclude that the abundance of LLP and NPLD species in Yangambi cannot be unambiguously attributed to past human disturbances or environmental variables. An alternative explanation is that present‐day forest composition is a result of adaptation to late‐Holocene drying. However, results are inconclusive and additional data are needed to confirm this alternative hypothesis.  相似文献   

8.
Biological data are often intrinsically hierarchical (e.g., species from different genera, plants within different mountain regions), which made mixed‐effects models a common analysis tool in ecology and evolution because they can account for the non‐independence. Many questions around their practical applications are solved but one is still debated: Should we treat a grouping variable with a low number of levels as a random or fixed effect? In such situations, the variance estimate of the random effect can be imprecise, but it is unknown if this affects statistical power and type I error rates of the fixed effects of interest. Here, we analyzed the consequences of treating a grouping variable with 2–8 levels as fixed or random effect in correctly specified and alternative models (under‐ or overparametrized models). We calculated type I error rates and statistical power for all‐model specifications and quantified the influences of study design on these quantities. We found no influence of model choice on type I error rate and power on the population‐level effect (slope) for random intercept‐only models. However, with varying intercepts and slopes in the data‐generating process, using a random slope and intercept model, and switching to a fixed‐effects model, in case of a singular fit, avoids overconfidence in the results. Additionally, the number and difference between levels strongly influences power and type I error. We conclude that inferring the correct random‐effect structure is of great importance to obtain correct type I error rates. We encourage to start with a mixed‐effects model independent of the number of levels in the grouping variable and switch to a fixed‐effects model only in case of a singular fit. With these recommendations, we allow for more informative choices about study design and data analysis and make ecological inference with mixed‐effects models more robust for small number of levels.  相似文献   

9.
    
In recent years, single‐cell sequencing (SCS) technologies have continued to advance with improved operating procedures and reduced cost, leading to increasing practical adoption among researchers. These emerging technologies have superior abilities to analyse cell heterogeneity at a single‐cell level, which have elevated multi‐omics research to a higher level. In some fields of research, application of SCS has enabled many valuable discoveries, and musculoskeletal system offers typical examples. This article reviews some major scientific issues and recent advances in musculoskeletal system. In addition, combined with SCS technologies, the research of cell or tissue heterogeneity in limb development and various musculoskeletal system clinical diseases also provides new possibilities for treatment strategies. Finally, this article discusses the challenges and future development potential of SCS and recommends the direction of future applications of SCS to musculoskeletal medicine.  相似文献   

10.
    
Question: Is there a light level at which alien grass biomass is reduced while still supporting growth and survival of native woody species, allowing for native species regeneration in abandoned pastures? Location: Island of Hawaii, USA. Methods: In a two‐part study we examined the effect of light availability on common native woody and alien grass species found in secondary forests in Hawaii. A field survey was conducted to examine the relationship between light availability and canopy type (open pasture, planted canopy and secondary forest) on understory grass biomass and litter accumulation. We then experimentally manipulated light levels to determine the effect of light availability on growth and survival of six native woody species and three alien grasses. Low‐light (5%), medium‐light (10%) and high‐light (20‐30%) treatments were created using shade structures erected beneath the existing secondary koa canopy. Results: In the field survey, alien grass biomass was greatest under the open pasture and lowest in the secondary forest. There was a positive correlation between understory light availability and alien grass biomass. In the experimental study, large reductions in relative growth rates were documented for all of the grass species and four of the six woody species under the lowest light level. Although growth at 5% light is substantially reduced, survival is still high (84‐100%), indicating that these species may persist under closed canopy. Conclusion: Low‐light conditions result in the greatest reduction in alien grass biomass while creating an environment in which native woody species can grow and survive.  相似文献   

11.
    
Environmental conditions during early‐life development can have lasting effects shaping individual heterogeneity in fitness and fitness‐related traits. The length of telomeres, the DNA sequences protecting chromosome ends, may be affected by early‐life conditions, and telomere length (TL) has been associated with individual performance within some wild animal populations. Thus, knowledge of the mechanisms that generate variation in TL, and the relationship between TL and fitness, is important in understanding the role of telomeres in ecology and life‐history evolution. Here, we investigate how environmental conditions and morphological traits are associated with early‐life blood TL and if TL predicts natal dispersal probability or components of fitness in 2746 wild house sparrow (Passer domesticus) nestlings from two populations sampled across 20 years (1994–2013). We retrieved weather data and we monitored population fluctuations, individual survival, and reproductive output using field observations and genetic pedigrees. We found a negative effect of population density on TL, but only in one of the populations. There was a curvilinear association between TL and the maximum daily North Atlantic Oscillation index during incubation, suggesting that there are optimal weather conditions that result in the longest TL. Dispersers tended to have shorter telomeres than non‐dispersers. TL did not predict survival, but we found a tendency for individuals with short telomeres to have higher annual reproductive success. Our study showed how early‐life TL is shaped by effects of growth, weather conditions, and population density, supporting that environmental stressors negatively affect TL in wild populations. In addition, shorter telomeres may be associated with a faster pace‐of‐life, as individuals with higher dispersal rates and annual reproduction tended to have shorter early‐life TL.  相似文献   

12.
    
We modeled 3D structures of all SARS‐CoV‐2 proteins, generating 2,060 models that span 69% of the viral proteome and provide details not available elsewhere. We found that ˜6% of the proteome mimicked human proteins, while ˜7% was implicated in hijacking mechanisms that reverse post‐translational modifications, block host translation, and disable host defenses; a further ˜29% self‐assembled into heteromeric states that provided insight into how the viral replication and translation complex forms. To make these 3D models more accessible, we devised a structural coverage map, a novel visualization method to show what is—and is not—known about the 3D structure of the viral proteome. We integrated the coverage map into an accompanying online resource (https://aquaria.ws/covid) that can be used to find and explore models corresponding to the 79 structural states identified in this work. The resulting Aquaria‐COVID resource helps scientists use emerging structural data to understand the mechanisms underlying coronavirus infection and draws attention to the 31% of the viral proteome that remains structurally unknown or dark.  相似文献   

13.
    
Transmission electron microscopy has historically been indispensable for virology research, as it offers unique insight into virus function. In the past decade, as cryo‐electron microscopy (cryo‐EM) has matured and become more accessible, we have been able to peer into the structure of viruses at the atomic level and understand how they interact with the host cell, with drugs or with antibodies. Perhaps, there was no time in recent history where cryo‐EM was more needed, as SARS‐CoV‐2 has spread around the globe, causing millions of deaths and almost unquantifiable economic devastation. In this concise review, we aim to mark the most important contributions of cryo‐EM to understanding the structure and function of SARS‐CoV‐2 proteins, from surface spikes to the virus core and from virus‐receptor interactions to antibody binding.  相似文献   

14.
50年来山东塔山植被与物种多样性的变化   总被引:3,自引:0,他引:3       下载免费PDF全文
高远  陈玉峰  董恒  郝加琛  慈海鑫 《生态学报》2011,31(20):5984-5991
为分析塔山植被与物种多样性50a自然演替和动态变化,2009-2010年,采用系统勘踏法和典型取样法进行了调查。当前塔山主要植被类型为\"黑松林-赤松林-栓皮栎林\"。50a间,该区针叶林从黑松(Pinus thunbergii)林演替为黑松林、赤松(P. densiflora)林和油松林(P. tabulaeformis)为主的混合针叶林,但针叶林的整体优势度下降,以栓皮栎(Quercus variabilis)和麻栎(Q. acutissima)为建群种的阔叶林面积明显增大,由针叶林向阔叶林的演替趋势明朗。物种丰富度为草本层>灌木层>乔木层,Shannon-wiener指数和Simpson指数为灌木层>草本层>乔木层,物种多样性较低,处于森林演替初期。  相似文献   

15.
The updating and rethinking of vegetation classifications is important for ecosystem monitoring in a rapidly changing world, where the distribution of vegetation is changing. The general assumption that discrete and persistent plant communities exist that can be monitored efficiently, is rarely tested before undertaking a classification. Marion Island (MI) is comprised of species‐poor vegetation undergoing rapid environmental change. It presents a unique opportunity to test the ability to discretely classify species‐poor vegetation with recently developed objective classification techniques and relate it to previous classifications. We classified vascular species data of 476 plots sampled across MI, using Ward hierarchical clustering, divisive analysis clustering, non‐hierarchical kmeans and partitioning around medoids. Internal cluster validation was performed using silhouette widths, Dunn index, connectivity of clusters and gap statistic. Indicator species analyses were also conducted on the best performing clustering methods. We evaluated the outputs against previously classified units. Ward clustering performed the best, with the highest average silhouette width and Dunn index, as well as the lowest connectivity. The number of clusters differed amongst the clustering methods, but most validation measures, including for Ward clustering, indicated that two and three clusters are the best fit for the data. However, all classification methods produced weakly separated, highly connected clusters with low compactness and low fidelity and specificity to clusters. There was no particularly robust and effective classification outcome that could group plots into previously suggested vegetation units based on species composition alone. The relatively recent age (c. 450,000 years B.P.), glaciation history (last glacial maximum 34,500 years B.P.) and isolation of the sub‐Antarctic islands may have hindered the development of strong vascular plant species assemblages with discrete boundaries. Discrete classification at the community‐level using species composition may not be suitable in such species‐poor environments. Species‐level, rather than community‐level, monitoring may thus be more appropriate in species‐poor environments, aligning with continuum theory rather than community theory.  相似文献   

16.
Rates of change in tree communities following major disturbances are determined by a complex set of interactions between local site factors, landscape history and structure, regional species pools and species life histories. Our analysis focuses on vegetation change following abandonment of agricultural fields or pastures, as this is the most extensive form of major disturbance in Neotropical forests. We consider five tree community attributes: stem density, basal area, species density, species richness and species composition. We describe two case studies, in northeastern Costa Rica and Chiapas, Mexico, where both chronosequence and annual tree dynamics studies are being applied. These case studies show that the rates of change in tree communities often deviate from chronosequence trends. With respect to tree species composition, sites of different ages differ more than a single site followed over time through the same age range. Dynamic changes in basal area within stands, on the other hand, generally followed chronosequence trends. Basal area accumulation was more linked with tree growth rates than with net changes in tree density due to recruitment and mortality. Stem turnover rates were poor predictors of species turnover rates, particularly at longer time-intervals. Effects of the surrounding landscape on tree community dynamics within individual plots are poorly understood, but are likely to be important determinants of species accumulation rates and relative abundance patterns.  相似文献   

17.
林火干扰对北方针叶林林下植被的影响   总被引:7,自引:0,他引:7       下载免费PDF全文
林下植被在北方针叶林植被群落中的物种多样性最高, 且具有较高的生物量周转率和地上部分净初级生产力, 对北方针叶林生态系统功能起着重要作用。火干扰是决定北方针叶林林下植被结构与功能的一个重要景观过程。该文综述了火干扰是如何通过与地形、火前林冠组成的交互作用而影响环境资源和林下植被的。最近的研究表明: 林下植被能够影响火后树木更新苗的定植、重建速率及森林演替轨迹; 林下植被还会通过影响元素的生物地球化学过程(凋落物降解和养分循环)影响林下环境资源的数量与异质性。因此, 研究火后初期北方针叶林林下植被的动态变化, 对于物种多样性保护和森林管理具有重要意义。  相似文献   

18.
 A secondary succession of vegetation on clearcut sites was studied in Western Sichuan. The coverage and biomass of trees, shrubs and herbs at different stages of succession have been surveyed. The result showed that the coverage and biomass of trees and shrubs have changed greatly in the succession. After the forest was cut, raspberry’s (Rubus daeus) coverage was the greatest during the first 0–15 years, Red birch’s coverage was the greatest during 16–29 years, while the total coverage of other shrubs was greater than those of raspberry and red birch during 10–20 years.The following empirical formulas with good fitness have been used:Ctree=0.803+2.347t1/2 (r=0.88 p<0.01) Cshrub=l0.481 l0.392T+0.373T2 (r=0.87 p<0.01)Cherb=0.489+87.001/T (r=0.93 p<0.01) C: biomass, kilogram/ha T: time period, year According to the curves, the succession of vegetation can be divided into four stages: herb stage. 0—3 years; raspberry stage: 4—10 year; shrub and small broad-leaved forest stage: 11—20 years, and small broad–leaved forest stage: 21—29 years.  相似文献   

19.
    
Roosting information is crucial to guiding bat conservation and bat‐friendly forestry practices. The Ryukyu tube‐nosed bat Murina ryukyuana (Endangered) and Yanbaru whiskered bat Myotis yanbarensis (Critically Endangered) are forest‐dwelling bats endemic to the central Ryukyu Archipelago, Japan. Despite their threatened status, little is known about the roosting ecology of these species and the characteristics of natural maternity roosts are unknown. To inform sustainable forestry practices and conservation management, we radio‐tracked day roosts of both species in the subtropical forests of Okinawa''s Kunigami Village District. We compared roost and roost site characteristics statistically between M. ryukyuana nonmaternity roosts (males or nonreproductive females), maternity roosts, and all M. yanbarensis roosts. Generalized linear models were used to investigate roost site selection by M. ryukyuana irrespective of sex and age class. Lastly, we compiled data on phenology from this and prior studies. Nonreproductive M. ryukyuana roosted alone and primarily in understory foliage. Murina ryukyuana maternity roosts were limited to stands >50 years old, and ~60% were in foliage. Myotis yanbarensis roosted almost entirely in cavities along gulch bottoms and only in stands >70 years old (~1/3 of Kunigami''s total forest area). Murina ryukyuana maternity roosts were higher (4.3 ± 0.6 m) than conspecific nonmaternity roosts (2.3 ± 0.5 m; p < .001) and M. yanbarensis roosts (2.7 ± 0.5 m; not significant). Model results were inconclusive. Both species appear to be obligate plant roosters throughout their life cycle, but the less flexible roosting preferences of M. yanbarensis may explain its striking rarity. To conserve these threatened bats, we recommend the following forestry practices: (a) reduce clearing of understory vegetation, (b) refrain from removing trees along streams, (c) promote greater tree cavity densities by protecting old‐growth forests and retaining snags, and (d) refrain from removing trees or understory between April and July, while bats are pupping.  相似文献   

20.
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