Species Abundance in a Forest Community in South China: A Case of Poisson Lognormal Distribution

Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m×20 m, 5 m×5 m, and 1 m×1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal;(ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (σ andμ) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the σ and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/σ should be an alternative measure of diversity.     

Repeatability of Quantitative Sodium Magnetic Resonance Imaging for Estimating Pseudo-Intracellular Sodium Concentration and Pseudo-Extracellular Volume Fraction in Brain at 3 T

The purpose of this study is to assess the repeatability of the quantification of pseudo-intracellular sodium concentration (C₁) and pseudo-extracellular volume fraction (α) estimated in brain in vivo using sodium magnetic resonance (MRI) at 3 T. Eleven healthy subjects were scanned twice, with two sodium MRI acquisitions (with and without fluid suppression by inversion recovery), and two double inversion recovery (DIR) proton MRI. DIR MRIs were used to create masks of gray and white matter (GM, WM), that were subsequently applied to the C₁ and α maps calculated from sodium MRI and a tissue three-compartment model, in order to measure the distributions of these two parameters in GM, WM or full brain (GM+WM) separately. The mean, median, mode, standard deviation (std), skewness and kurtosis of the C₁ and α distributions in whole GM, WM and full brain were calculated for each subject, averaged over all data, and used as parameters for the repeatability assessment. The coefficient of variation (CV) was calculated as a measure of reliability for the detection of intra-subject changes in C₁ and αfor each parameter, while intraclass correlation (ICC) was used as a measure of repeatability. It was found that the CV of most of the parameters was around 10–20% (except for C₁ kurtosis which is about 40%) for C₁ and α measurements, and that ICC was moderate to very good (0.4 to 0.9) for C₁ parameters and for some of the α parameters (mainly skewness and kurtosis). In conclusion, the proposed method could allow to reliably detect changes of 50% and above of the different measurement parameters of C₁ and αin neuropathologies (multiple sclerosis, tumor, stroke, Alzheimer’s disease) compared to healthy subjects, and that skewness and kurtosis of the distributions of C₁ and αseem to be the more sensitive parameters to these changes.     

A measure of species diversity related to the lognormal distribution of individuals among species

An investigation has been made of the relation between species diversity and the lognormal distribution of individuals among species, using phytoplankton samples from the Indian Ocean. The area under the truncated lognormal curve representing a sample gives the total number of species, S, while the logarithmic standard deviation, σ, gives a measure of the scatter of distribution of individuals among species, the other factor affecting diversity. Using a method described by Hald, truncated lognormal curves were fitted to the phytoplankton data and estimates obtained for the mean, ξ, the logarithmic standard deviation, σ, the number of species in the modal octave, N_o, and the number of species in the population universe, N. Since one is interested in a sample only in so far as it reflects the properties of the population from whence it came, estimated population parameters were used to define measures of diversity by which means it was hoped to obtain a diversity index independent of sample size, i.e., a diversity value related more to the population than to the sample.     

Nitrogen Fixed By Cyanobacteria Is Utilized By Deposit-Feeders

Benthic communities below the photic zone depend for food on allochthonous organic matter derived from seasonal phytoplankton blooms. In the Baltic Sea, the spring diatom bloom is considered the most important input of organic matter, whereas the contribution of the summer bloom dominated by diazotrophic cyanobacteria is less understood. The possible increase in cyanobacteria blooms as a consequence of eutrophication and climate change calls for evaluation of cyanobacteria effects on benthic community functioning and productivity. Here, we examine utilization of cyanobacterial nitrogen by deposit-feeding benthic macrofauna following a cyanobacteria bloom at three stations during two consecutive years and link these changes to isotopic niche and variations in body condition (assayed as C:N ratio) of the animals. Since nitrogen-fixing cyanobacteria have δ¹⁵N close to -2‰, we expected the δ¹⁵N in the deposit-feeders to decrease after the bloom if their assimilation of cyanobacteria-derived nitrogen was substantial. We also expected the settled cyanobacteria with their associated microheterotrophic community and relatively high nitrogen content to increase the isotopic niche area, trophic diversity and dietary divergence between individuals (estimated as the nearest neighbour distance) in the benthic fauna after the bloom. The three surface-feeding species (Monoporeia affinis, Macoma balthica and Marenzelleria arctia) showed significantly lower δ¹⁵N values after the bloom, while the sub-surface feeder Pontoporeia femorata did not. The effect of the bloom on isotopic niche varied greatly between stations; populations which increased niche area after the bloom had better body condition than populations with reduced niche, regardless of species. Thus, cyanobacterial nitrogen is efficiently integrated into the benthic food webs in the Baltic, with likely consequences for their functioning, secondary production, transfer efficiency, trophic interactions, and intra- and interspecific competition.     

Species Abundance in a Forest Community in South China：A Case of Poisson Lognormal Distribution

Abstract: Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m× 20 m, 5 m× 5 m, and 1 m× 1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal; (ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (& and μ) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the α and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/α should be an alternative measure of diversity.
(Managing editor: Ya-Qin HAN)     

A Note on Measures of Multivariate Kurtosis

We propose a measure of multivariate kurtosis suggested from Mardia's measure of multivariate skewness b₁,p, and examine its relationship both to Mardia's measure of multivariate kurtosis b₂,p, and to a smooth test of multivariate kurtosis ǔ₄².     

Rank Diversity of Languages: Generic Behavior in Computational Linguistics

Statistical studies of languages have focused on the rank-frequency distribution of words. Instead, we introduce here a measure of how word ranks change in time and call this distribution rank diversity. We calculate this diversity for books published in six European languages since 1800, and find that it follows a universal lognormal distribution. Based on the mean and standard deviation associated with the lognormal distribution, we define three different word regimes of languages: “heads” consist of words which almost do not change their rank in time, “bodies” are words of general use, while “tails” are comprised by context-specific words and vary their rank considerably in time. The heads and bodies reflect the size of language cores identified by linguists for basic communication. We propose a Gaussian random walk model which reproduces the rank variation of words in time and thus the diversity. Rank diversity of words can be understood as the result of random variations in rank, where the size of the variation depends on the rank itself. We find that the core size is similar for all languages studied.     

Patterns of ramet population of Iris japonica Thunb. and their effects on herb diversity in different microsites on Jinyun Mountain, China

Spatial patterns of ramet population of Iris japonica Thunb. and their effect on species diversity in the herb layer of 3 microsites (open area of forest edge (OAFE), bamboo forest (BF) and evergreen broad-leaved forest (EBF)) on Jinyun Mountain were studied using spatial pattern, niche and diversity analyses in a combination of population and community methods. The results were as follows: (1) judged by V/m and Morisita index (Iδ), ramet population of I. japonica in 3 microsites all clumped from scale 0.5 m × 0.5 m to 2 m × 2 m; (2) the pattern scale and pattern intensity both gradually decreased on all scales, and the density of ramet population of I. japonica decreased with the increase in canopy density and the decrease in relative photon flux density (RPFD) and R/FR from OAFE to EBF. In OAFE and BF, widespread I. japonica had significantly negative influence on the dominance of original dominant species and on species diversity in the herb layer (p < 0.05), while those influences in EBF were extremely weak. The mechanisms that pattern characteristics of ramet population of I. japonica influence herb diversity in 3 microsites were different. In OAFE, strong regeneration niche (above-ground spatial and below-ground root) and trophic niche (nutrient) competition had significantly negative influence on the species diversity of rare herbs and dwarf herbs. In BF, strong regeneration niche (below-ground root) and trophic niche (above-ground for light and below-ground for nutrient) competition had negative effect on the occurrence of rare species and on the survival of other herb species. In EBF, weak niche competition had little effect on the survival of herb species. Intensity of regeneration niche and trophic niche competition between I. japonica and other herb species is the determinant to the mechanism that ramet population of I. japonica influences herb diversity.     

On the relationship between Pielou’s evenness and landscape dominance within the context of Hill’s diversity profiles

Entropy-related biodiversity indices deriving their conceptual basis from Shannon’s information theory have a long history of use in ecology for quantifying community structure and diversity. In addition, in the last two decades, numerous information–theoretical indices, such as the landscape dominance index, have been extensively applied to characterize landscape diversity in space and time. In this contribution, we offer a simple analytical relation between Pielou’s evenness J and landscape dominance D within the broader context of Hill’s parametric diversity family. Within this context, we recommend the use of Hill’s diversity number evenness E_1,0 to overcome the shortcomings both of Pielou’s evenness J and the landscape dominance index D.     

Microbial minorities modulate methane consumption through niche partitioning

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity–ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.     

Interpreting Ecological Diversity Indices Applied to Terminal Restriction Fragment Length Polymorphism Data: Insights from Simulated Microbial Communities

Ecological diversity indices are frequently applied to molecular profiling methods, such as terminal restriction fragment length polymorphism (T-RFLP), in order to compare diversity among microbial communities. We performed simulations to determine whether diversity indices calculated from T-RFLP profiles could reflect the true diversity of the underlying communities despite potential analytical artifacts. These include multiple taxa generating the same terminal restriction fragment (TRF) and rare TRFs being excluded by a relative abundance (fluorescence) threshold. True community diversity was simulated using the lognormal species abundance distribution. Simulated T-RFLP profiles were generated by assigning each species a TRF size based on an empirical or modeled TRF size distribution. With a typical threshold (1%), the only consistently useful relationship was between Smith and Wilson evenness applied to T-RFLP data (TRF-E_var) and true Shannon diversity (H′), with correlations between 0.71 and 0.81. TRF-H′ and true H′ were well correlated in the simulations using the lowest number of species, but this correlation declined substantially in simulations using greater numbers of species, to the point where TRF-H′ cannot be considered a useful statistic. The relationships between TRF diversity indices and true indices were sensitive to the relative abundance threshold, with greatly improved correlations observed using a 0.1% threshold, which was investigated for comparative purposes but is not possible to consistently achieve with current technology. In general, the use of diversity indices on T-RFLP data provides inaccurate estimates of true diversity in microbial communities (with the possible exception of TRF-E_var). We suggest that, where significant differences in T-RFLP diversity indices were found in previous work, these should be reinterpreted as a reflection of differences in community composition rather than a true difference in community diversity.     

Animal-sediment relationships in intertidal marine benthic habitats: Some determinants of deposit-feeding species diversity

Particulate sedimentary properties were examined in a variety of New England intertidal habitats. The sediments were composed of a complex array of both food and non-food particle types. Little evidence of temporal or vertical spatial variation was observed in the major particulate fractions. Organic-mineral aggregates (“detritus”), however, exhibited significant seasonal change in abundance at the sediment-water interface, possibly being related to annual productivity-decay cycles of the marsh grass Spartina alterniflora. Both particulate and bulk sedimentary characteristics were related to deposit-feeding species diversity. Species richness was correlated with the amount of surficial sedimentary organic carbon, and species diversity with total particulate and food particulate diversity. Food abundance and variety, therefore, may regulate the organization of deposit-feeding assemblages. Standard methods for describing sediments may largely be inadequate for understanding many aspects of organism-sediment relationships in marine benthic environments.     

The Choice of PCR Primers Has Great Impact on Assessments of Bacterial Community Diversity and Dynamics in a Wastewater Treatment Plant

Assessments of bacterial community diversity and dynamics are fundamental for the understanding of microbial ecology as well as biotechnological applications. We show that the choice of PCR primers has great impact on the results of analyses of diversity and dynamics using gene libraries and DNA fingerprinting. Two universal primer pairs targeting the 16S rRNA gene, 27F&1492R and 63F&M1387R, were compared and evaluated by analyzing the bacterial community in the activated sludge of a large-scale wastewater treatment plant. The two primer pairs targeted distinct parts of the bacterial community, none encompassing the other, both with similar richness. Had only one primer pair been used, very different conclusions had been drawn regarding dominant phylogenetic and putative functional groups. With 27F&1492R, Betaproteobacteria would have been determined to be the dominating taxa while 63F&M1387R would have described Alphaproteobacteria as the most common taxa. Microscopy and fluorescence in situ hybridization analysis showed that both Alphaproteobacteria and Betaproteobacteria were abundant in the activated sludge, confirming that the two primer pairs target two different fractions of the bacterial community. Furthermore, terminal restriction fragment polymorphism analyses of a series of four activated sludge samples showed that the two primer pairs would have resulted in different conclusions about community stability and the factors contributing to changes in community composition. In conclusion, different PCR primer pairs, although considered universal, target different ranges of bacteria and will thus show the diversity and dynamics of different fractions of the bacterial community in the analyzed sample. We also show that while a database search can serve as an indicator of how universal a primer pair is, an experimental assessment is necessary to evaluate the suitability for a specific environmental sample.     

Diversity and distribution of hidden cultivable fungi associated with marine animals of Antarctica

In the present study, we surveyed the distribution and diversity of fungal assemblages associated with 10 species of marine animals from Antarctica. The collections yielded 83 taxa from 27 distinct genera, which were identified using molecular biology methods. The most abundant taxa were Cladosporium sp. 1, Debaryomyces hansenii, Glaciozyma martinii, Metschnikowia australis, Pseudogymnoascus destructans, Thelebolus cf. globosus, Pseudogymnoascus pannorum, Tolypocladium tundrense, Metschnikowia australis, and different Penicillium species. The diversity, richness, and dominance of fungal assemblages ranged among the host; however, in general, the fungal community, which was composed of endemic and cold-adapted cosmopolitan taxa distributed across the different sites of Antarctic Peninsula, displayed high diversity, richness, and dominance indices. Our results contribute to knowledge about fungal diversity in the marine environment across the Antarctic Peninsula and their phylogenetic relationships with species that occur in other cold, temperate, and tropical regions of the World. Additionally, despite their extreme habitats, marine Antarctic animals shelter cryptic and complex fungal assemblages represented by endemic and cosmopolitan cold-adapted taxa, which may represent interesting models to study different symbiotic associations between fungi and their animal hosts in the extreme conditions of Antarctica.     

黄土丘陵区沙棘群落封育过程中物种多样性动态

对黄土丘陵区子午岭不同封育年限沙棘群落的高等植物多样性特征进行了初步分析。结果表明：不同封育阶段沙棘群落灌木层和草本层的物种多样性指数表现出大致相同的趋势,即草本层>灌木层。同一层次的物种多样性指数D和H′虽然数值不同,但在不同封育阶段沙棘群落有基本一致的趋势,灌木层物种多样性指数基本上随封育时间的增加而增加;草本层多样性指数在荒草地阶段较高,其他阶段的沙棘群落随封育时间的增加而减少。随着群落封育,群落相似性增加。总体上,随着沙棘群落的封育,不同科属的植物种类在增加,群落生态优势度增加,群落趋向稳定。采取封禁措施,减少人为干扰,是沙棘群落封育的有效途径。     

不同干扰对黄土区典型草原物种多样性和生物量的影响

对黄土区典型草原进行封育+施肥(EF)、封育+火烧(EB)、封育(E)和放牧(G)处理,实地调查分析群落盖度、高度、密度、地上现存量和物种多样性,以研究不同干扰对黄土区典型草原群落物种多样性和生物量的影响.结果表明:在4种干扰类型中,施肥+封育草地群落盖度和地上生物量最高,且优势度指数最高,这与禾本科草占优势地位有关,群落均匀度指数和多样性指数最低,符合“生态位理论”;放牧地群落高度、盖度、密度和地上现存量最低,群落丰富度指数和多样性指数最高,支持“中度干扰理论”;封育地密度和均匀度指数最高;具体表现为:4种干扰类型地上生物量的变化趋势为封育+施肥＞封育+火烧＞封育＞放牧;说明长时间的封育对草地是一种严重干扰.群落丰富度指数(R和Ma)的排列顺序为放牧＞封育+施肥＞封育+火烧＞封育,群落物种多样性指数(H'和D)的排列顺序为放牧＞封育＞封育+火烧＞封育+施肥,优势度指数与多样性指数相反,群落均匀度指数(Jsw和Ea)的排列顺序为封育＞放牧＞封育+火烧＞封育+施肥.不同干扰样地群落生产力与Shannon-Wiener和Simpson 多样性指数间呈负相关关系,这个结论可以用地上/地下竞争的相互作用来解释.     

The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community,Mexico

Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as “Endangered” on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.     

EEG and Cognitive Biomarkers Based Mild Cognitive Impairment Diagnosis

Objective

Recently, Electroencephalogram (EEG) shows potential in the diagnosis of Alzheimer's disease and other dementia. We aim to investigate whether EEG and selected cognitive biomarkers can classify mild cognitive impairment (MCI), dementia and healthy subjects using support vector machine classifier in Indian cohort.

Habitat preference in the dark-eyed junco (Junco hyemalis): The role of photoperiod and dominance

Wild-caught dark-eyed juncos (Junco hyemalis), simultaneously presented with projected slides of their winter and summer habitats, demonstrated distinct preferences (in terms of time spent in front of particular slides) consistent with their season of capture and prior laboratory experience. Juncos caught in and kept on winter or summer photoperiods preferred winter and summer habitat slides respectively. A gradual increase in photoperiod up to natural summer conditions induced a switch from winter to summer habitat preference: a decrease in photoperiod induced a range of slide preferences correlated with the junco's size, a measure of the bird's dominance rank.