Corrections to the indices of community dissimilarity based on species diversity measures

Summary A number of indices of community dissimilarity based on the species diversity measures have been proposed during the last three decades (Margalef 1956, 1957; Kohn 1959; MacArthur 1965; Horn 1966; Glowaciski and Järvinen 1975; Järvinen and Väisänen 1976). Each of them is measuring the wrong quantity if the value of diversity in a particular sample is higher than in a pooled sample. Simple corrections are suggested to avoid this shortcoming.     

The dissimilarity of species interaction networks

In a context of global changes, and amidst the perpetual modification of community structure undergone by most natural ecosystems, it is more important than ever to understand how species interactions vary through space and time. The integration of biogeography and network theory will yield important results and further our understanding of species interactions. It has, however, been hampered so far by the difficulty to quantify variation among interaction networks. Here, we propose a general framework to study the dissimilarity of species interaction networks over time, space or environments, allowing both the use of quantitative and qualitative data. We decompose network dissimilarity into interactions and species turnover components, so that it is immediately comparable to common measures of β‐diversity. We emphasise that scaling up β‐diversity of community composition to the β‐diversity of interactions requires only a small methodological step, which we foresee will help empiricists adopt this method. We illustrate the framework with a large dataset of hosts and parasites interactions and highlight other possible usages. We discuss a research agenda towards a biogeographical theory of species interactions.     

Examination of association indices and formulation of a composite seasonal dissimilarity index

1) A composite seasonal dissimilarity index (SD) is developed to compare systematically changing communities. 2) Seven association indices were examined. Percent Dissimilarity was chosen for community comparisons because it retained a large percentile range for scaling dissimilar communities and responded linearly to the degree of overlap between communities. 3) Examination of three consecutive years of Lake Ontario phytoplankton data, using SD, produced reasonable dissimilarity values. Inter-year variability was significantly greater than inter-station variability. 4) SD has great potential in ecology for comparing communities which vary along any gradient.     

Possibilities to improve the genetic evaluation of a rare breed using limited genomic information and multivariate BLUP

The use of molecular genetic information in the evaluation of livestock has become more common. This study looks at the efficacy of using such information to improve the genetic evaluation of a rare breed of dual-purpose cattle. Data were available in the form of pedigree information on the Gloucester cattle breed in the United Kingdom and recorded milk and beef performance on a small number of animals. In addition, molecular genetic information in the form of multi-marker, multiple regression results converted to a 1 to 10 score (Igenity scores) and 123 single nucleotide polymorphism (SNP) genotypes for 199 non-recorded animals were available. Appropriate mixed-animal models were explored for the recorded traits and these were used to calculate estimated breeding values (EBV), and their accuracies, for 6527 animals in the breed’s pedigree file. Various ways to improve the accuracy of these EBV were explored. This involved using multivariate BLUP analyses, genomic estimated breeding values (GEBV) and combining Igenity scores with recorded traits in a series of bivariate genetic analyses. Using the milk recording traits as an example, the accuracy of a number of traits could be improved using multivariate analyses by up to 14%, depending on the combination of traits used. The level of increase in accuracy largely corresponded to the absolute difference between the genetic and residual correlations between two traits, but this was not always symmetrical. The use of GEBV did not increase the accuracy of milk trait EBV owing to the low proportion of variance explained by the 101 SNPs used. Using Igenity scores in bivariate analyses with the recorded data was more successful in increasing EBV accuracy. The largest increases were found in genotyped animals with no recorded performance (e.g. a 58% increase in fat weight in milk); however, the size of the increase depended on the level of the genetic correlation between the recorded trait and the Igenity score for that trait. Lower levels of improvements in accuracy were seen in animals that were recoded but not genotyped, and ancestors which were neither genotyped nor recorded. This study demonstrated that it was possible to improve the accuracy of EBV estimation by including Igenity score information in genetic analyses but it also concluded that increasing the level of performance recording in the breed would be beneficial.     

Decline of rare and specialist species across multiple taxonomic groups after grassland intensification and abandonment

Traditionally managed mountain grasslands are declining as a result of abandonment or intensification of management. Based on a common chronosequence approach we investigated species compositions of 16 taxonomic groups on traditionally managed dry pastures, fertilized and irrigated hay meadows, and abandoned grasslands (larch forests). We included faunal above- and below-ground biodiversity as well as species traits (mainly rarity and habitat specificity) in our analyses. The larch forests showed the highest species number (345 species), with slightly less species in pastures (290 species) and much less in hay meadows (163 species). The proportion of rare species was highest in the pastures and lowest in hay meadows. Similar patterns were found for specialist species, i.e. species with a high habitat specificity. After abandonment, larch forests harbor a higher number of pasture species than hay meadows. These overall trends were mainly supported by spiders and vascular plants. Lichens, bryophytes and carabid beetles showed partly contrasting trends. These findings stress the importance to include a wide range of taxonomic groups in conservation studies. All in all, both abandonment and intensification had similar negative impacts on biodiversity in our study, underlining the high conservation value of Inner-Alpine dry pastures.     

Assessing the functional turnover of species assemblages with tailored dissimilarity matrices

It is often suggested that community functional diversity is an appropriate predictive measure of ecosystem functioning, particularly if relevant species traits for the ecological property of interest are carefully selected. However, methods for selecting traits are often based on expert knowledge or on theoretical models of ecosystem functioning, but usually do not include explicitly developed quantitative procedures. Here we propose to construct a so‐called ‘tailored dissimilarity matrix’ between species assemblages to emphasize their functional turnover in response to some user‐defined ecological property. First, a subset of community weighted mean trait values (CWM) is selected by stepwise regression on the ecological process of interest. The selected CWM values are then replaced by the residuals of the least‐squares regressions of each single CWM on the ecological process of interest and pairwise Euclidean distances between the residual values at each sampling site are calculated. We illustrate the advantages of the tailored approach using two distinct plant and bee communities under contrasting fire regimes in temperate forests of southern Switzerland. Our results demonstrated that, unlike for the original CWM values, the tailored approach optimized the degree of functional differentiation among bee and plant species assemblages, i.e. the species functional turnover, with respect to different fire regimes.     

Biocenotic activity of salmonellae of rare groups

The symbiotic activity of 69 Salmonella cultures of rare groups, belonging to the strains of different origin, with respect to pathogenic and nonpathogenic bacteria, bacilli, Staphylococcus aureus was studied. The study revealed that salmonellae of rare groups were capable of synergetic activity with respect to all test cultures used in this study. The spectrum and manifestation of this property were found to depend on the origin of the strains. The direction of the synergetic activity of salmonellae of rare groups, isolated from the environment, made it possible to suggest the importance of this sign for their survival under unfavorable environmental conditions. Close relationship between the synergetic activity of microorganisms and the clinical course of infection gave grounds for the conclusion on the pathogenic importance of this property and the necessity of its study in the evaluation of the pathogenic potential of microorganisms.     

Genetic dissimilarity of putative gamma-ray-induced 'Preciosa-AAAB-Pome type' banana (Musa sp) mutants based on multivariate statistical analysis

Bananas are among the most important fruit crops worldwide, being cultivated in more than 120 countries, mainly by small-scale producers. However, short-stature high-yielding bananas presenting good agronomic characteristics are hard to find. Consequently, wind continues to damage a great number of plantations each year, leading to lodging of plants and bunch loss. Development of new cultivars through conventional genetic breeding methods is hindered by female sterility and the low number of seeds. Mutation induction seems to have great potential for the development of new cultivars. We evaluated genetic dissimilarity among putative 'Preciosa' banana mutants generated by gamma-ray irradiation, using morphoagronomic characteristics and ISSR markers. The genetic distances between the putative 'Preciosa' mutants varied from 0.21 to 0.66, with a cophenetic correlation coefficient of 0.8064. We found good variability after irradiation of 'Preciosa' bananas; this procedure could be useful for banana breeding programs aimed at developing short-stature varieties with good agronomic characteristics.     

Evaluating indices of body condition in two cricket species

Body mass components (dry mass, lean dry mass, water mass, fat mass) in each sex correlate strongly with body mass and pronotum length in Gryllus texensis and Acheta domesticus. Ordinary least squares (OLS) regression underestimates the scaling relationship between body mass and structural size (i.e., pronotum length) in both cricket species compared with standard major axis (SMA) regression. Standardized mass components correlate more strongly with scaled mass index () than with residual body mass (R_i). R_i represents the residuals from an OLS regression of log body mass against log pronotum length. Neither condition index predicts energy stores (i.e., fat content) in G. texensis. R_i is not correlated with energy stores in A. domesticus whereas is negatively correlated. A comparison of condition index methods using published data showed that neither sex nor diet quality affected body condition at adulthood in G. texensis when using the scaled mass index. However, the residual index suggested that sex had a significant effect on body condition. Further, analysis of covariance (ANCOVA) suggested that diet quality significantly affects body mass while statistically controlling for body size (i.e., body condition). We conclude that the statistical assumptions of condition index methods must be met prior to use and urge caution when using methods that are based on least squares in the y‐plane (i.e., residual index ANCOVA).     

Functional groups of rare plants differ in levels of imperilment

Comparative examination of a large sample of plant species can reveal important aspects of life history that influence the ecology and distribution of taxa and their vulnerability to local extinction. We investigated whether functional groups of 71 rare plant species with contrasting life history traits differed in terms of population losses over time, regional range contraction, and range-wide levels of imperilment. Using town-level occurrence data from herbaria and Natural Heritage Program databases, we characterized species' extents of occurrence as α-hulls encompassing the centroids of New England towns that contained well-documented populations of these rare taxa. Family affiliation was used as a covariate in analyses to reduce phylogenetic bias. Disparate functional groups of plants differed both in proportions of populations lost and declines in range areas over time, with insect-pollinated taxa, upland (vs. wetland) taxa, species with localized seed dispersal modes, and taxa reaching their northern range boundary in New England significantly more imperiled than other functional groups. These techniques permit a broad comparative assessment of the distribution of large numbers of plant taxa, so that we can identify several functional groups that warrant more concerted conservation attention.     

The population ecology of rare species

There is no general theory of rarity, although one is sorely needed both to understand population dynamics and to determine conservation priorities. Here we suggest some of the strands that might be woven into such a theory. They include relationships between local abundance, geographic range size and body size of species, and the determinants of minimum viable population sizes. In each of these areas much can still be learnt from the classical 'compare and contrast' approach using assemblages of species from a variety of taxa. Freshwater fish have contributed relatively little to the broad ecological literature in this respect. We perform some tentative analyses for this group of species, and speculate on how they might fit into our current understanding of rarity.     

高寒草甸种间性状差异和物种均匀度对物种多样性与功能多样性关系的影响

物种多样性(SD)与功能多样性(FD)之间存在多种关系,但由于生态系统功能主要由物种的功能属性决定,因而功能多样性对生态系统功能的影响大于物种多样性的影响。但在种间性状差异和物种均匀度这两个构成功能多样性的基本成分中,何者对功能多样性影响更大,并进而决定SD-FD关系尚不明确。通过在高寒矮嵩草(Kobresia humilis)草甸为期6a的刈割(留茬1 cm、3 cm及不刈割)和施肥(尿素7.5 g m~(-2)a~(-1)+磷酸二胺1.8 g m~(-2)a~(-1)、不施肥)控制实验,研究了种间性状差异(33个物种13个性状)和物种均匀度(所有物种)对物种多样性(所有物种)与功能多样性(33个物种13个性状)之间关系的影响。研究结果显示:(1)物种多样性与功能多样性正相关,它们与多性状种间差异负相关,而与物种均匀度正相关。物种均匀度是导致功能多样性变化的主要因素,也是导致SD-FD正相关的原因,这是因为随着物种多样性增加,物种均匀度的增加程度大于多性状种间差异的减少程度,因而功能多样性增加,SD-FD正相关;(2)功能多样性指数(FD_(Rao)和FDis)随物种多样性指数(H')减速递增,表明群落存在一定的功能冗余,且功能冗余随物种多样性的增大而增大,但尚未达到产生SD-FD无相关性的极限H'值;(3)功能多样性对高寒草甸生态系统地上净初级生产力(ANPP)的影响大于物种多样性的影响,二元线性回归显示在同时考虑二者对ANPP的影响时,可排除物种多样性的作用。但由于物种多样性下降或物种丧失引起的物种功能性状丢失或性状空间维度减小将导致功能多样性降低,表明它们之间存在一定互补性,在研究生物多样性与生态系统功能关系时,同时考虑物种多样性和功能多样性的影响仍十分必要。     

Engineering of microorganisms towards recovery of rare metal ions

The bioadsorption of metal ions using microorganisms is an attractive technology for the recovery of rare metal ions as well as removal of toxic heavy metal ions from aqueous solution. In initial attempts, microorganisms with the ability to accumulate metal ions were isolated from nature and intracellular accumulation was enhanced by the overproduction of metal-binding proteins in the cytoplasm. As an alternative, the cell surface design of microorganisms by cell surface engineering is an emerging strategy for bioadsorption and recovery of metal ions. Cell surface engineering was firstly applied to the construction of a bioadsorbent to adsorb heavy metal ions for bioremediation. Cell surface adsorption of metal ions is rapid and reversible. Therefore, adsorbed metal ions can be easily recovered without cell breakage, and the bioadsorbent can be reused or regenerated. These advantages are suitable for the recovery of rare metal ions. Actually, the cell surface display of a molybdate-binding protein on yeast led to the enhanced adsorption of molybdate, one of the rare metal ions. An additional advantage is that the cell surface display system allows high-throughput screening of protein/peptide libraries owing to the direct evaluation of the displayed protein/peptide without purification and concentration. Therefore, the creation of novel metal-binding protein/peptide and engineering of microorganisms towards the recovery of rare metal ions could be simultaneously achieved.     

Morphological clues to genetic species: multivariate analysis of greater Galago sibling species

Several studies conducted in diverse fields indicate the presence of a genetic discontinuity within the taxon Galago crassicaudatus E. Geoffroy--the thick-tailed bushbaby. One of these areas is morphology. This contribution details a statistical analysis of skull material classified under this taxon in order 1) to confirm the objective existence of two morphotypes, and 2) to investigate the characters that allow the skull types to be distinguished. Emphasis is placed on multivariate techniques, although univariate and bivariate techniques are included where they are felt to be appropriate. All statistical analyses point to the reality of the morphological discontinuity between the groups. This is true even when size considerations have been reduced by rescaling the data. The results support separation of the populations at a specific level: G. crassicaudatus and G. garnettii. In addition, the structural changes observed in the two taxa--including an increase in overall size in G. crassicaudatus--are indicative of a divergence in preferred habitats: G. garnettii is adapted to more mesic environmental conditions, and to a softer, less fibrous diet than is its more robust sibling.