Measuring size and composition of species pools: a comparison of dark diversity estimates

Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat‐specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so‐called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co‐occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co‐occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods need attention, especially when dark diversity is estimated at the plot level.     

Forest vascular plants as indicators of plant species richness: A data analysis of a flora atlas from northwestern Germany

Abstract

Our study had the objective to examine whether the number of forest vascular plants in a forest-poor region may be indicative of total plant species richness and of the number of threatened plant species. We also related forest plant species richness to geological and soil variables. The analysis was based on a regional flora atlas from the Weser-Elbe region in northwestern Germany including incidence data of species in a total of 1109 grid cells (each ca. 2.8 × 2.8 km²). All taxa were classified either as forest or non-forest species. Total species richness in the grid cells ranged from 65 to 597, with a mean value of 308. The number of forest species varied between 20 and 309 (mean 176). Grid cells with or without particular geological units differed in total and forest species richness, with those containing peatland and marshland being particularly species-poor. Indicator value analysis showed that both total and forest species richness in the grid cells were related to soil acidity and nitrogen in a hump-backed manner, with the highest number of species found at moderately low values for nitrogen and at intermediate values of pH. Forest species richness was highly positively correlated with the number of non-forest species and threatened non-forest species. Indicators for high species richness were primarily those species that are confined to closed semi-natural forests with a varied topography and relatively base- and nutrient-rich soils. Grid cells including historically ancient forest exhibited a higher species richness than grid cells lacking ancient forest, indicating the importance of a long habitat continuity for a high phytodiversity. The “habitat coincidence” of high species richness is best explained by similar responses of forest species and species of other habitats to the main environmental gradients. It is suggested that the regional patterns found for the Weser-Elbe region can be transferred also to other forest-poor regions in Central Europe.     

Tree species composition and diversity in Miombo woodlands between co‐managed and government‐managed regimes,Malawi

Comparative information on the composition and diversity in tree species associations in Miombo woodland is limited. This study assessed how tree species associations across forest reserves of Miombo woodland in Malawi varied in composition and diversity concerning site factors and resource use disturbances under co‐management versus government management. Eighty nested circular plots, randomly selected in ArcGIS, were sampled to record stem diameter at breast height (DBH) of tree species: 0.04 ha for stems 5–29.9 cm DBH and 0.16 ha for stems ≥30 cm DBH. The recorded 109 tree species grouped into communities and 14 sub‐communities, using stem counts by species in TWINSPAN analysis. Sub‐divisions to level 5 showed eigenvalues ≥0.3, symbolising the stability of sub‐divisions. North/South sub‐divisions related to site factors; historical/current resource use influenced differences at levels 3–5. Species importance differed, indicating few important species in each sub‐community. Brachystegia and Julbernardia species showed importance across sub‐communities while Uapaca sansibarica in government management. Disturbances stimulated high species diversity. Recommendations include the need for a policy review towards group‐felling mature stands to stimulate regeneration and selective thinning of suppressed stems in stand development stages to maintain species diversity, productive recovery, diverse resource use value, and monitoring of harvesting impacts.     

The influence of environmental factors and management methods on the vegetation of mesic grasslands in a central European mountain range

We examined how environmental factors combined with the diverse ways of the extensive management of mesic mountain grasslands affect species composition and diversity in the Polish part of Central Sudetes Mts. Based on the data from 100 research plots altitude, organic matter content and exchangeable magnesium in the soil, as well as the maximum soil water capacity and amount of sand fraction significantly affected species composition. Among the management methods, a significant effect on the differentiation of species composition was observed following the cessation of usage and mowing. Mown meadows had the highest share of forbs in the biomass, whereas those abandoned ones were dominated by tall and expansive grasses, mainly Calamagrostis epigejos. The species richest grasslands occurred in areas with soils of high water capacity, containing high concentrations of calcium and low amounts of total nitrogen. No significant effect of management methods on the total number of species as well as on the number of forb species was observed. Mown pastures had the highest mean value of the Shannon–Wiener diversity index.     

Clonal growth and plant species abundance

Background and Aims

Both regional and local plant abundances are driven by species'' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden.

Methods

Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates.

Key Results

After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level.

Conclusions

Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden performance parameters provide a practical approach to assessing the roles of clonal growth morphological traits (and LHS traits) for large sets of species.     

Evaluating the ecological realism of plant species distribution models with ecological indicator values

Species distribution models (SDMs) are routinely applied to assess current as well as future species distributions, for example to assess impacts of future environmental change on biodiversity or to underpin conservation planning. It has been repeatedly emphasized that SDMs should be evaluated based not only on their goodness of fit to the data, but also on the realism of the modeled ecological responses. However, possibilities for the latter are hampered by limited knowledge on the true responses as well as a lack of quantitative evaluation methods. Here we compared modeled niche optima obtained from European-scale SDMs of 1476 terrestrial vascular plant species with empirical ecological indicator values indicating the preferences of plant species for key environmental conditions. For each plant species we first fitted an ensemble SDM including three modeling techniques (GLM, GAM and BRT) and extracted niche optima for climate, soil, land use and nitrogen deposition variables with a large explanatory power for the occurrence of that species. We then compared these SDM-derived niche optima with the ecological indicator values by means of bivariate correlation analysis. We found weak to moderate correlations in the expected direction between the SDM-derived niche optima and ecological indicator values. The strongest correlation occurred between the modeled optima for growing degree days and the ecological indicator values for temperature. Correlations were weaker for SDM-derived niche optima with a more distal relationship to ecological indicator values (notably precipitation and soil moisture). Further, correlations were consistently highest for BRT, followed by GLM and GAM. Our method gives insight into the ecological realism of modeled niche optima and projected core habitats and can be used to improve SDMs by making a more informed selection of environmental variables and modeling techniques.     

Timing of snowmelt affects species composition via plant strategy filtering

Plant strategy schemes aim to classify plants according to measurable traits and group species according to their shared evolutionary responses to selective pressures. In this way, it becomes possible to make meaningful comparisons among ecosystems and communities and to predict how plant communities might respond to changes in their environment. Here, we classified common alpine plants which occur in snowpatches (Early and Late snowmelt sites) and in adjacent vegetation (Snow-free sites which melt early in the growing season) using Grime’s CSR plant strategy scheme. Alpine plant communities are largely driven by environmental filters associated with a relatively constant gradient of snowmelt timing. Since snow persistence influences the abiotic environment and plant assemblages alike, we hypothesised that these patterns would be reflected in community CSR scores. Weighted community CSR scores were clustered towards the stress-tolerator (S) corner of the triangular CSR space, and Snow-free communities were significantly more stress-tolerant than Early and Late snowmelt communities. This suggests that snowpatch communities are functionally distinct from surrounding vegetation when considering the major axes of plant variation identified by CSR theory. These results lend further support to the importance of the timing of snowmelt as a key filter, influencing how species and plant strategy types distribute themselves across the alpine landscape.     

杉木林改造成乡土阔叶林对林下植物物种组成和多样性的影响

把杉木林改造成乡土阔叶林,不仅能提供高价值木材,而且能够提升生态系统服务功能,是我国目前改造退化针叶林最常见的经营模式之一,但这些改变对其林下植物物种组成和多样性的影响及机制我们尚知之甚少。以南亚热带杉木林采伐迹地上重新种植的杉木林、红锥林和米老排林为研究对象,调查研究其灌木层和草本层植物物种组成和多样性,结果表明：（1）和杉木林相比,改造后的红锥林和米老排林灌木层的植物物种丰富度和多样性均呈极显著降低（P<0.01）,但其草本层植物只有物种丰富度极显著降低（P<0.01）,多样性均无显著变化（P>0.05）;（2）主成分分析（PCA）表明改造后的林分灌木层和草本层的植物物种组成发生明显的变化,冗余分析（RDA）确定导致林分灌木层植物物种组成发生变化的主要原因是杉木林改造成红锥林和米老排林后的冠层透光率、土壤碳氮比、土壤含水量和凋落物碳氮比的显著变化,而冠层透光率和土壤碳氮比的显著变化是导致其林下草本层植物物种组成发生明显变异的主要因子;（3）方差分解结果显示微地形、乔木特性和土壤理化性质的独立效应对灌木层和草本层植物物种组成的影响高于它们的交互效应。该研究为科学经营管理人工林和提高人工林生态系统多功能性提供科学依据。     

应用指示种预测森林管理对物种多样性及群落组成的影响

采用指示种分析方法,研究了会同亚热带森林物种多样性和群落组成对森林管理的响应.从357个林下种中鉴定出显著性指示种94个,并构造新的指示种数据集,检验指示种数据集和源群落数据集之间的关联,评估指示种对林下植被管理效应的预测潜能.结果表明:指示种数据集和源群落数据集之间存在极显著的关联(Mantel r=0.898),指示种数据集很好地预测了生物多样性的变化(回归分析,R2>0.74);指示种很好地预测了群落组成对森林管理的响应(ANOVA,F>16.79);非度量多尺度排序(NMDS)以及K-means聚类分析表明,对于不同森林管理的样地类型,指示种数据集的识别能力和源群落数据集是一致的.从物种多样性、群落组成以及在森林类型的识别上,指示种数据集和源群落数据集有一致性规律,作用几乎相同,因此森林评估可以利用指示种代替源群落预测森林管理效应,以减少森林全面调查的成本.     

干扰对植物群落物种组成及多样性的影响

在介绍了干扰的概念及其性质和干扰对物种多样性影响的有关假说基础上,以森林干扰为主要对象,探讨了干扰对植物群落物种组成的影响,并从干扰类型、干扰强度和干扰频率等几个方面阐述了干扰对植物群落物种多样性的影响;另外,还分析了重要的小尺度干扰——林隙在该方面的影响。分析总结出干扰对植物群落的影响差异主要与干扰特征、植物群落特征及植物的生物学特性和受干扰地点的资源条件有关。最后,总结分析了国内外在该方面研究存在的问题,并对今后研究提出一些建议,为相关工作提供参考。     

Using biological traits to assess how urbanization filters plant species of small woodlands

Question: Which biological traits (persistence, regeneration, dispersion traits and resource requirements) may explain the distribution of woodland flora along an urban–rural gradient? Location: The study was carried out in three medium‐sized conurbations of north‐western France: Angers, Nantes and Rennes. Methods: We sampled the vegetation of 36 small woodlands of about 1.5 ha composed of non‐planted vegetation along an urban–rural gradient. We characterized the position of woodlands along the urban–rural gradient by examining adjacent land cover. By using an ordination analysis (RLQ), we analysed which traits out of –23 tested were related to the contrasted distribution of species along the urban–rural gradient. Results: Species that are more likely to be found in urban woodlands than rural woodlands have different persistence traits (higher specific leaf area, more often rosette or semi‐rosette form, less underground vegetative multiplication), resource requirements (affinity for base‐rich and fertile soils) and regeneration traits (short life‐span). Dispersion traits were not related to the distribution of species along the urban–rural gradient. Conclusions: Our approach identifies traits that can help to determine the vulnerability of forest species as a result of the environmental changes that follow urbanization. Limiting the influence of the urban environment on habitat quality (particularly disturbance and soil enrichment) is likely to be of major importance in maintaining the plant biodiversity in woodlands.     

Interactive effects between plant functional types and soil factors on tundra species diversity and community composition

Plant communities are coupled with abiotic factors, as species diversity and community composition both respond to and influence climate and soil characteristics. Interactions between vegetation and abiotic factors depend on plant functional types (PFT) as different growth forms will have differential responses to and effects on site characteristics. However, despite the importance of different PFT for community assembly and ecosystem functioning, research has mainly focused on vascular plants. Here, we established a set of observational plots in two contrasting habitats in northeastern Siberia in order to assess the relationship between species diversity and community composition with soil variables, as well as the relationship between vegetation cover and species diversity for two PFT (nonvascular and vascular). We found that nonvascular species diversity decreased with soil acidity and moisture and, to a lesser extent, with soil temperature and active layer thickness. In contrast, no such correlation was found for vascular species diversity. Differences in community composition were found mainly along soil acidity and moisture gradients. However, the proportion of variation in composition explained by the measured soil variables was much lower for nonvascular than for vascular species when considering the PFT separately. We also found different relationships between vegetation cover and species diversity according the PFT and habitat. In support of niche differentiation theory, species diversity and community composition were related to edaphic factors. The distinct relationships found for nonvascular and vascular species suggest the importance of considering multiple PFT when assessing species diversity and composition and their interaction with edaphic factors. Synthesis: Identifying vegetation responses to edaphic factors is a first step toward a better understanding of vegetation–soil feedbacks under climate change. Our results suggest that incorporating differential responses of PFT is important for predicting vegetation shifts, primary productivity, and in turn, ecosystem functioning in a changing climate.     

人为干扰对风水林群落林下木本植物组成和多样性的影响

华南地区的风水林是乡村聚落的一种特色林分, 具有守护村庄的象征意义。在过去的数百年中, 风水林在乡村的社会文化习俗的影响下而受到保护, 对当地的生物多样性保育有着重要作用。为揭示人为干扰对风水林的影响, 我们选择广东省东莞市大岭山镇同一林分起源的3个具有相似地形的风水林, 研究了在不同干扰强度下其林下木本植物种类组成和物种多样性。多响应置换过程(multi-response permutation procedures, MRPP)分析表明, 人为干扰显著改变了风水林林下木本植物组成(P = 0.001, A = 0.3886), 沿着干扰由弱至强的梯度呈现出中生性植物减少、阳生性植物递增的趋势。多样性指数变化趋势为重度干扰＞中度干扰＞轻度干扰, 但没有表现出统计学意义上的差异(P＞0.05)。随着干扰强度的增大, 3个风水林群落相互间的林下物种相似性降低, 物种替代率呈增加趋势。双向聚类分析较好地反映出林下物种因受不同人为干扰强度影响而表现出在空间分布上的差异。指示种分析进一步确定了不同干扰强度下具有显著指示值(IV ≥60)的指示种。综合分析表明, 人为干扰有利于阳性物种在风水林内定居生长, 并明显地改变了林下木本植物组成, 但未能引起物种多样性的显著差异。此外, 找出对人为干扰产生关键生态响应的林下指示种, 对增进风水林的生物多样性保育以及生态系统管理有着重要的理论意义和实践价值。