Assessing the relative contribution of functional divergence and guild aggregation to overall functional structure of species assemblages

The study of functional structure in species assemblages emphasizes the detection of significant guild aggregation patterns. Thus, protocols based on intensive resampling of empirical data have been proposed to assess guild structure. Such protocols obtain the frequency distribution of a given functional similarity metric, and identify a threshold value (often the 95th percentile) beyond which clusters in a functional dendrogram are considered as significant guilds (using one-tailed tests). An alternative approach sequentially searches for significant differences between clusters at decreasing levels of similarity in a dendrogram until one is detected, then assumes that all subsequent nodes should also be significant. Nevertheless, these protocols do not test both the significance and sign of deviations from random at all levels of functional similarity within a dendrogram. Here, we propose a new bootstrapping approach that: (1) overcomes such pitfalls by performing two-tailed tests for each node in a dendrogram of functional similarity after separately determining their respective sample distributions, and (2) enables the quantification of the relative contribution of guild aggregation and functional divergence to the overall functional structure of the entire assemblage. We exemplify this approach by using long-term data on guild dynamics in a vertebrate predator assemblage of central Chile. Finally, we illustrate how the interpretation of functional structure is improved by applying this new approach to the data set available.     

Functional regularity: a neglected aspect of functional diversity

Functional diversity has been identified as a key to understanding ecosystem and community functioning. However, due to the lack of a sound definition its nature and measurement are still poorly understood. In the same way that species diversity can be split into species richness and species evenness, so functional diversity can be split into functional richness (i.e. the amount of functional trait/character/attribute space filled) and functional evenness (i.e. the evenness of abundance distribution in functional trait space). We propose a functional regularity index (FRO) as a measure of functional evenness for situations where species are represented only by a single functional trait value (e.g. mean, median or mode), and species abundances are known. This new index is based on the Bulla O index of species evenness. When dealing with functional types or categorical functional traits, the Bulla O or any other accepted species evenness index may be used directly to measure functional evenness. The advantage of FRO is that it supplies a measure of functional evenness for continuous trait data. The FRO index presented in this paper fulfils all the a priori criteria required. We demonstrate with two example datasets that a range of FRO values may be obtained for both plant and animal communities. Moreover, FRO was strongly related to ecosystem function as seen in photosynthetic biomass in plant communities, and was able to differentiate sampling stations in a lagoon based on the functional traits of fish. Thus, the FRO index is potentially a highly useful tool for measuring functional diversity in a variety of ecological situations.     

Adaptation and functional integration in primate phylogenetics

In two areas of phylogenetics, contrary predictions have been developed and maintained for character analysis and weighting. With regard to adaptation, many have argued that adaptive characters are poorly suited to phylogenetic analysis because of a propensity for homoplasy, while others have argued that complex adaptive characters should be given high weight because homoplasy in complex characters is unlikely. Similarly, with regard to correlated sets of characters, one point of view is that such sets should be collapsed into a single character-a single piece of phylogenetic evidence. Another point of view is that a suite of correlated characters should be emphasized in phylogenetics, again because recurrence of detailed similarity in the same suite of features is unlikely. In this paper, I discuss the theoretical background of adaptation and functional integration with respect to phylogenetic systematics of primates. Several character examples are reviewed with regard to their functional morphology and phylogenetic signal: postorbital structures, tympanic morphology, fusion of the mandibular symphysis, the tooth comb, strepsirrhine talar morphology, and the prehensile tail. It is clear when considering characters such as these that some characters are synapomorphic of major clades and at the same time functionally important. This appears particularly to be the case when characters are integrated into a complex and maintained as stable configurations. Rather than being simply a problem in character analysis, processes of integration may help to explain the utility of phylogenetically informative characters. On the other hand, the character examples also highlight the difficulty in forming a priori predictions about a character's phylogenetic signal. Explanations of patterns of character evolution are often clade-specific, which does not allow for a simple framework of character selection and/or weighting.     

反硝化菌功能基因及其分子生态学研究进展

由微生物推动的反硝化作用是地球氮素循环的重要分支,尽管已被发现广泛存在于细菌、真菌和古生菌中,其功能基因的研究仍仅限于很少几个物种。现代分子生物学的发展为研究环境微生物提供了行之有效的方法,以反硝化功能基因作为分子标记的分子生态学研究迅猛发展。综述近年来国内外微生物反硝化功能基因研究及以其为标记的分子生态学研究进展。     

RNA干扰文库在功能基因组学研究中的发展及应用

RNA干扰（RNAi）是双链RNA分子在mRNA水平上诱发的序列特异性转录后基因表达沉默,从基因组水平设计针对多个靶基因的RNAi序列,建立RNAi文库进行系统性、大规模的筛选工作是功能基因组学研究的有力工具。目前RNAi文库主要包括质粒（或病毒）文库、siRNA表达盒文库、寡核苷酸文库和随机RNAi文库,已经被成功应用于基因功能鉴别、信号转导途径解析和药物靶标筛选等研究领域。近年来,这一领域发展迅速,本文就RNAi文库的发展应用以及存在的问题与展望进行综述。     

The functional importance of rare and dominant species in a Neotropical forest bird community

Bird communities in Tropical forests have high rate of rare species, but only recently some studies suggested their disproportional role for the overall functional diversity. We investigated data from bird communities monitored annually using point counts over ten years in Iguassu National Park, that is a large and protected area in the southern portion of the Atlantic Forest in Brazil. We aimed (1) to determine the rare and dominant species in the community based on their abundance over time; (2) to evaluate the impact of each class of rarity on the overall functional volume of the community; (3) to investigate the pattern of occupancy of the trait space filled by each dominance class, and (4) to assess the disparity in functional trait composition between classes of rarity. We defined dominant, intermediate, and rare species in communities using cluster analysis and data of relative abundance of species in five sections of 1-km in the forest interior. The number of clusters was defined in accordance with the silhouette criterion measures of cohesion and separation that range from −1 to 1, with values > 0.5 indicating high-quality clusters. Among total 138 bird species recorded, 107 were rare, 26 intermediates, and 5 dominants. Our data corroborate a functional disproportional importance of rare bird species in the community considering the functional space (FRic), but functional dispersion (FDis) was not significantly different between the rare and intermediate species. In fact, there is a large overlap of the functional volume occupied by rare in relation to dominant/intermediate species. The niche space occupied by rare species covers most of the space occupied by intermediate and dominant species. The low representativeness of functional turnover indicates that few functions are unique to the classes of higher dominance. Our data suggest the importance of rare bird species to the overall functional diversity but also highlights the potential use of dominants/intermediates species as indicators to select important forests areas for conservation, as certain forest fragments. Through these most abundant species it would be possible to assess which functions are heaviest in abundance, becoming core functions, in the context of each independent forest fragment.     

Plant functional types and disturbance dynamics – Introduction

Abstract. Plant functional traits and types are useful concepts in relation to disturbance responses of natural and managed ecosystems. To explore their applicability in greater depth, a set of 12 papers presents a broad range of issues from methodologies to the results of particular trait studies in the field, and modelling approaches. So far, empirical studies have only allowed us to identify a few functional traits that are consistently associated with disturbance. To determine the trait variations associated with climate, disturbance history and current disturbance regime as well as the interactions between these factors, global-scale comparisons of numerous individual studies are required. Significant advances toward this ambitious goal are presented in these papers, and include: (1) the articulation of experimental and analytical methodologies for individual studies that could usefully contribute to a global comparison; (2) the identification of core traits that can be used in the further search for disturbance-related traits common to a range of environments; (3) further information on vegetation response to disturbance in terms of trait representation, and the identification of attribute syndromes; (4) the identification of issues for modelling disturbance dynamics using functional types.     

Structural and functional diversities in lepidopteran serine proteases

Primary protein-digestion in Lepidopteran larvae relies on serine proteases like trypsin and chymotrypsin. Efforts toward the classification and characterization of digestive proteases have unraveled a considerable diversity in the specificity and mechanistic classes of gut proteases. Though the evolutionary significance of mutations that lead to structural diversity in serine proteases has been well characterized, detailing the resultant functional diversity has continually posed a challenge to researchers. Functional diversity can be correlated to the adaptation of insects to various host-plants as well as to exposure of insects to naturally occurring antagonistic biomolecules such as plant-derived protease inhibitors (PIs) and lectins. Current research is focused on deciphering the changes in protease specificities and activities arising from altered amino acids at the active site, specificity-determining pockets and other regions, which influence activity. Some insight has been gained through in silico modeling and simulation experiments, aided by the limited availability of characterized proteases. We examine the structurally and functionally diverse Lepidopteran serine proteases, and assess their influence on larval digestive processes and on overall insect physiology. Invited paper     

Ecological indicators and functional groups of copepod assemblages

Copepods are important ecological indicators of ecosystem functioning. In this study, we analyzed the structure of copepod assemblages and cross-shelf patterns based on functional traits and indicator value analysis. Copepod samples were collected from 54 stations distributed along the inner, middle, and outer continental shelves covering a wide geographical area (20,100 km²). Overall, 38 species were identified: 20 Calanoida, 14 Cyclopoida, and 4 Harpacticoida. Copepod density was the highest in the inner shelf profile, with richness and diversity being higher on the outer shelf close to the shelf break. The results suggest that there is a gradient of zooplankton distribution even on narrow (<50 km) continental shelves. The cluster analysis of the stations showed a tendency to form three groups largely corresponding to physical location. Two major functional groups were identified, sorted by spawning strategy. These were subdivided according to the trophic regime and feeding strategy. Temora turbinata (alien species), Clausocalanus furcatus, and Ditrichocorycaeus amazonicus (native species) were found to be ecological indicators. These species have different functional traits and distinct cross-shelf distributions, where the alien species dominates the turbid coastal waters, and C. furcatus is an indicator of outer-shelf waters. Thus, these species can be considered ecological indicators of the different continental shelf waters. The results indicate that it is necessary to understand the functional diversity and ecological indicators of copepods, considering their importance for the basis of marine food webs.     

Microwear and morphology: functional relationships between human dental microwear and the mandible

Microscopic pits and scratches form on teeth during chewing, but the extent to which their formation is influenced by mandibular morphology is unknown. Digitized micrographs of the base of facet nine of the first, second, and third mandibular molar were used to record microwear features from an archaeological sample of modern humans recovered from Semna South in northern Sudan (n=38; 100 BC to AD 350). Microwear patterns of the molar row are correlated with mandibular corpus width and depth, and with mandibular length. Variations in shear and compression at the base of facet nine during chewing were inferred. It may be that some correlations between microwear and mandibular morphology are predictable, reflecting similar aspects of masticatory loading, though the full extent of the relationship remains to be resolved.     

Decreasing functional responses as a result of adaptive consumer behavior

Summary Several different mechanisms that may produce decreasing functional responses are investigated using models that assume that an optimally foraging consumer is exploiting one or two resources. Decreasing functional responses are associated with situations in which there are costs to resource consumption. If the process of resource acquisition has costs, decreasing functional responses may occur when there is a single homogeneous resource. If the cost is solely a function of the amount of resource ingested, decreasing functional responses on a single resource do not occur. Both types of cost can produce decreasing functional responses when there are two resource types and a trade-off relationship between consumption of one and consumption of the other. Decreasing functional responses seem to be most likely to occur on a food that yields high benefits and costs per unit of foraging time or effort when there is an alternative resource which yields low benefits and costs. Given this type of foraging choice, the functional response is most likely to decrease when the benefits of ingestion increase at a decreasing rate, and the costs of ingestion increase at an increasing rate with amount ingested. An important and unique consequence of decreasing functional responses is the possibility of population cycles in differential equation models of consumer-resource systems with non-reproducing resources; this is illustrated with a simple comsumer-resource model.     

Semiparametric estimation for joint modeling of colorectal cancer risk and functional biomarkers measured with errors

This research is motivated by a pilot colorectal adenoma study, where the outcome of interest is the presence of colorectal adenoma representing risk for colorectal cancer, and the predictors of interest are protein biomarkers that are repeatedly measured with errors along the length of a microscopic structure in the human colon, the colon crypt. Biomarkers of this type are referred to as functional biomarkers. The investigators are interested in identifying features of functional biomarkers that are associated with risk for colorectal cancer. In this paper, we investigate a joint modeling approach, where the binary clinical outcome is modeled using a logistic regression model with the unobserved true functional biomarkers as the predictors. Most existing methods are developed either for linear models or for functional biomarkers measured without errors and cannot be directly applied to our data. The applicable methods include a two-step method and a maximum likelihood method, which have some limitations. We propose a robust semiparametric method to overcome the limitations of the existing methods. We study the properties of the proposed method, and show in simulations that it compares favorably with other methods and also offers significant savings in CPU time. We analyze the pilot colorectal adenoma data and show that expression levels of AFC, a tumor suppressor gene, in the transitional area from the proliferation zone to the differentiation zone of colon crypts are likely to be associated with risk for colorectal cancer. Given the relatively small sample size in the pilot study, our results need to be validated in the future full-scale studies.     

A functional assessment of the response of grassland vegetation to reduced grazing and abandonment

Question: Predicting the impact of land‐use change on vegetation is vital to understanding how biodiversity and ecosystem function may respond. Is it correct to assume that abandonment is an extreme form of grazing reduction? Location: Borders and central Scotland. Methods: The analysis used data sets from two identical experiments where the impacts of two unfertilized, extensively grazed treatments and one unfertilized abandoned treatment were compared against the species dynamics of a pasture subject to normal, productive grazing management over a 16‐year period. Initial multivariate analysis using Principal Response Curves was used to assess if particular traits were associated with either extensive or abandoned treatments, and was checked using univariate tests of individual traits. RLQ analysis followed by clustering into response groups was used to assess if species behaved in a similar manner between sites. Results: For many traits/attributes the shift in value or proportion was approximately linear across the extensification treatments as grazing was removed. However, certain traits showed step changes and quadratic responses. Leaf dry matter content, an important effect trait, was in the latter group. Most traits/attributes and species behaved similarly at the two sites. However, traits such as regenerative strategy, seed length, longevity and mass and seed bank type behaved differently, indicating that they are not predictable response traits. Conclusion: The results indicate that responses to grazing removal during extensification are largely straightforward and largely independent of species pool. However, there are discrepancies that suggest that simple analyses of the impacts of land‐use changes such as grazing reduction may hide more complex responses.     

New characters for the functional interpretation of primate scapulae and proximal humeri

The study of muscle function in nonhuman primates through the technique of electromyography (EMG) has facilitated the identification of specific functional roles for muscles in particular behaviors. This has led to a more complete understanding of the biomechanics of certain regions of the musculoskeletal system, and should facilitate our ability to identify morphological features useful in the functional interpretation of fossil material. The current paper represents one such investigation of a new set of morphometric characters of the scapula and proximal humerus suggested by EMG analyses of shoulder muscle function. A set of new metric variables were examined on the scapulae and proximal humeri of 25 species of extant anthropoid primates, as well as on casts of scapulae and humeri of three fossil primate taxa. The variables are primarily related to the line of action and attachments of the rotator cuff muscles. The position of the scapular spine, the degree of lateral expansion of the subscapular fossa, the size and shape of the subscapularis insertion facet on the lesser tubercle, and the orientation of the infraspinatus insertion facet on the greater tubercle all appear to successfully sort the extant taxa into locomotor groups. Their appearance on the fossil specimens generally supports previous functional interpretations of each taxon's locomotor abilities based on a variety of other characters, suggesting that these traits are equally applicable to fossil material. © Wiley-Liss, Inc.