Sylvain Dolédec

ADE-4: a multivariate analysis and graphical display software

We present ADE-4, a multivariate analysis and graphical display software. Multivariate analysis methods available in ADE-4 include usual one-table methods like principal component analysis and correspondence analysis, spatial data analysis methods (using a total variance decomposition into local and global components, analogous to Moran and Geary indices), discriminant analysis and within/between groups analyses, many linear regression methods including lowess and polynomial regression, multiple and PLS (partial least squares) regression and orthogonal regression (principal component regression), projection methods like principal component analysis on instrumental variables, canonical correspondence analysis and many other variants, coinertia analysis and the RLQ method, and several three-way table (k-table) analysis methods. Graphical display techniques include an automatic collection of elementary graphics corresponding to groups of rows or to columns in the data table, thus providing a very efficient way for automatic k-table graphics and geographical mapping options. A dynamic graphic module allows interactive operations like searching, zooming, selection of points, and display of data values on factor maps. The user interface is simple and homogeneous among all the programs; this contributes to making the use of ADE-4 very easy for non- specialists in statistics, data analysis or computer science.

Matching species traits to environmental variables: a new three-table ordination method

This paper addresses the question of studying the joint structure of three data tablesR,L andQ. In our motivating ecological example, the central tableL is a sites-by-species table that contains the number of organisms of a set of species that occurs at a set of sites. At the margins ofL are the sites-by-environment data tableR and the species-by-trait data table Q. For relating the biological traits of organisms to the characteristics of the environment in which they live, we propose a statistical technique calledRLQ analysis (R-mode linked toQ-mode), which consists in the general singular value decomposition of the triplet (RtDILDJQ,Dq,Dp) whereDI,DJ,Dq,Dp are diagonal weight matrices, which are chosen in relation to the type of data that is being analyzed (quantitative, qualitative, etc.). In the special case where the central table is analysed by correspondence analysis,RLQ maximizes the covariance between linear combinations of columns ofR andQ. An example in bird ecology illustrates the potential of this method for community ecologists.

NICHE SEPARATION IN COMMUNITY ANALYSIS: A NEW METHOD

The design and objective of a community study imply the selection of the appropriate ordination technique in terms of species response models and weighting options. In this paper, we start from the observation that existing two-table ordination techniques and related measures of niche breadth inevitably weight a sample in proportion to its abundance. We introduce a new multivariate method, which gives a more even weight to all sampling units, including those which are species poor or individual poor. We use this new method of analysis which we call OMI (for Outlying Mean Index) to address the question of niche separation and niche breadth. The Outlying Mean Index, or species marginality, measures the distance between the mean habitat conditions used by species (species centroid), and the mean habitat conditions of the sampling area (origin of the niche hyperspace), and OMI analysis places species along habitat conditions using a maximization of their mean OMI. Therefore, the position of the species depends on their niche deviation from a reference, which represents neither the mean nor the most abundant species, but a theoretical ubiquitous species that tolerates the most general habitat conditions (i.e., a hypothetical species uniformly distributed among habitat conditions). We demonstrate that OMI analysis is well suited for the investigation of multidimensional niche breadths in the case of strong limiting factors (e.g., meteorological conditions) or strong driving forces (e.g., longitudinal stream gradient). Furthermore, the analysis helps in finding which eco- logical factors are most important for community structure and organization and provides a separation of species based on their niche characteristics.

EFFECT OF LAND DISTURBANCE AND STRESS ON SPECIES TRAITS OF GROUND BEETLE ASSEMBLAGES

In this paper we test whether the morphology and life traits of species (in our case ground beetles of the family Carabidae) can be related to the main underlying axes of environmental variability of their habitats. Sites were selected a priori to maximize two gradients: land use as a general measure of disturbance characterized by an index of land management, and habitat adversity or stress as characterized by elevation and vegetation structure. The underlying environmental axes and the relationships of the morphology and life traits of the species with them were investigated using RLQ analysis, a multivariate ordination method able to relate a species trait table to a site characteristics table by way of a species abundance table. The first environmental axis was highly statistically significant and explained most of the variability. It was strongly negatively related to the intensity of land management, and positively related to increasing elevation and a set of variables reflecting vegetation stress. Two predictions were tested and found to be valid in the studied system: in highly managed lowland sites species were smaller, and the frequency of macropterous species (with better dispersal abilities) was higher. Other traits also showed significant relationships with the main environmental axis: in the intensively managed lowland sites species had broader bodies, longer trochanters, and wider femora (characters associated with plant eaters), were paler in color, overwintered only as adults, bred in spring or autumn, and were active in summer. We conclude that the ground beetle assemblages of the studied sites respond in a similar way to the same underlying environmental factors. This allows the precise definition of functional groups, which can be used to characterize functional diversity and its relationships with changes in land management.

Functional traits as indicators of biodiversity response to land use changes across ecosystems and organisms.

Rigorous and widely applicable indicators of biodiversity are needed to monitor the responses of ecosystems to global change and design effective conservation schemes. Among the potential indicators of biodiversity, those based on the functional traits of species and communities are interesting because they can be generalized to similar habitats and can be assessed by relatively rapid field assessment across eco-regions. Functional traits, however, have as yet been rarely considered in current common monitoring schemes. Moreover, standardized procedures of trait measurement and analyses have almost exclusively been developed for plants but different approaches have been used for different groups of organisms. Here we review approaches using functional traits as biodiversity indicators focussing not on plants as usual but particularly on animal groups that are commonly considered in different biodiversity monitoring schemes (benthic invertebrates, collembolans, above ground insects and birds). Further, we introduce a new framework based on functional traits indices and illustrate it using case studies where the traits of these organisms can help monitoring the response of biodiversity to different land use change drivers. We propose and test standard procedures to integrate different components of functional traits into biodiversity monitoring schemes across trophic levels and disciplines. We suggest that the development of indicators using functional traits could complement, rather than replace, the existent biodiversity monitoring. In this way, the comparison of the effect of land use changes on biodiversity is facilitated and is expected to positively influence conservation management practices.

Perspectives for biomonitoring at large spatial scales: a unified measure for the functional composition of invertebrate communities in European running waters

Summary Environmental policies increasingly focus on the enhancement of ecological functions across large geographical areas and thus call for biomonitoring tools that assess these functions at large spatial scales. A potential answer to this call would be to use general biological traits of organisms that indicate ecological functions, as such traits will be comparable among communities even across biogeographic regions that differ in their taxonomic composition. Here, we used benthic invertebrates and European running waters as example to illustrate how multiple biological traits could provide a measure for the large-scale biomonitoring of the functional composition of communities. Our measure considered the relative abundance of 63 categories of 11 biological traits (such as size, reproductive and dispersal potential, food and feeding habits) that indicate various ecological functions. Comparing this measure for 10 most natural French reference regions with 37 other most natural regions/stream types scattered across Europe demonstrated an extremely high spatial and temporal stability of the functional composition of natural invertebrate communities at the European scale. Thus, our functional measure corresponds to a fundamental standard for a large-scale biomonitoring tool, which is the stable and reliable indication of the natural reference state across ecoregions that differ more or less in their taxonomic composition. Applying our functional measure to regulated stream sites below dams (in England, Finland and Spain) and to streams receiving sewage inputs (in Wales, Poland and Sardinia) demonstrated highly significant (p −6 ) differences in the functional composition between the human-impacted and the natural reference communities. In addition, some of the trait categories responded in a consistently contrasting way to each of the two types (regulation, sewage) of human impact. Consequently, our measure for the functional composition of invertebrate communities provides a first unified European baseline for future stream and river management: it was stable in the most natural but otherwise very different running water types across Europe, it safely indicated human impact, and it could potentially discriminate specific types of human disturbances. As all living organisms have multiple biological traits, our approach could serve to generate, for other types of communities and ecosystems, a set of large-scale biomonitoring tools that use similar and perhaps even comparable measures for the functional community composition. Umweltpolitik konzentriert sich zunehmend auf die grosraumige Verbesserung okologischer Funktionen und fordert deshalb Bioindikatorsysteme, die diese Funktionen grosraumig bewerten. Eine potentielle Antwort auf diese Forderung konnte die Benutzung funktioneller, allgemein biologischer Merkmale von Organismen sein, da solche Merkmale zwischen Lebensgemeinschaften verschiedener biogeographischer Regionen vergleichbar sind, selbst wenn sich die Regionen in ihrer taxonomischen Zusammensetzung unterscheiden. Am Beispiel benthischer Wirbelloser und europaischer Fliesgewasser zeigen wir, wie eine Vielzahl von biologischen Merkmalen als Mas fur eine grosraumige Bioindikation der funktionellen Zusammensetzung von Lebensgemeinschaften dienen kann. Unser Mas basiert auf der relativen Haufigkeit von 63 Kategorien in 11 biologischen Merkmalen (z.B. Korpergrose, Reproduktions- und Dispersionspotential, Nahrung und Ernahrungsweise), die verschiedene okologische Funktionen indizieren. Ein Vergleich dieses Mases von 10 besonders naturnahen franzosischen Referenzregionen und 37 anderen, uber ganz Europa verteilten, besonders naturnahen Regionen/Flieswassertypen zeigte eine extrem hohe raumliche und zeitliche Stabilitat der funktionellen Zusammensetzung naturlicher Wirbellosengemeinschaften im gesamten europaischen Raum. Somit entspricht unser funktionelles Mas einer Grundanforderung an ein grosraumiges Bioindikatorsystem: die stabile und zuverlassige Indikation des naturlichen Referenzzustandes fur verschiedene Okoregionen, die sich mehr oder minder in der taxonomischen Zusammensetzung unterscheiden. Die Anwendung unseres funktionellen Mases auf regulierte Flieswasserabschnitte unterhalb von Staudammen (in England, Finnland und Spanien) sowie auf abwasserempfangende Fliesgewasser (in Wales, Polen und auf Sardinien) zeigte hochsignifikante (p −6 ) Abweichungen in der funktionellen Zusammensetzung zwischen durch den Menschen beeinflusten und naturlichen Lebensgemeinschaften. Zusatzlich veranderten sich einige Kategorien der biologischen Merkmale ubereinstimmend gegensatzlich fur jeden der beiden Typen (Regulation, Abwasser) menschlicher Einflusse. Unser Mas der funktionellen Zusammensetzung von Wirbellosengemeinschaften schafft folglich eine erste einheitliche Basis fur ein zukunftiges Flieswassermanagement in Europa: es war stabil in besonders naturnahen aber ansonsten sehr verschiedenen Flieswassertypen des gesamten europaischen Raumes, es indizierte verlaslich menschliche Einflusse und es konnte auf verschiedene spezifische menschliche Storungen unterschiedlich reagieren. Da alle lebenden Organismen eine Vielzahl biologischer Merkmale aufweisen, sollte unser Ansatz auf andere Typen von Lebensgemeinschaften und Okosystemen ubertragbar sein. Er konnte fur diese verschiedenen Typen eine Serie von grosraumigen Bioindikatorsystemen schaffen, die ahnliche und vielleicht sogar vergleichbare Mase fur die funktionelle Zusammensetzung von Lebensgemeinschaften benutzen.

Quantifying Disturbance in Streams: Alternative Measures of Disturbance in Relation to Macroinvertebrate Species Traits and Species Richness

Appropriate tests of disturbance theory require that disturbance is defined and measured in an organism-related sense. We quantified 7 measures of disturbance, 3 dealing with the pattern of disturbance of the stream bed (assessed using painted tracer particles), 3 dealing with aspects of discharge variation and 1 being a subjective composite measure of stream channel stability (Pfankuchs index). Hypotheses relating to invertebrate taxon richness (maximal at intermediate levels of disturbance) and the representation of particular insect species traits (assemblages in more disturbed sites contain higher percentages of individuals possessing high adult mobility and streamlined-flattened larval morphology) were both supported when disturbance was measured in terms of bed movement but generally not when measured in terms of discharge variation. When disturbance was estimated by Pfankuchs index, species trait predictions were supported but the taxon richness prediction was not. A co-inertia analysis, searching for a co-structure between our environmental and faunistic data sets, allowed us to distinguish taxa that apparently are resistant to bed movement from taxa that appear to be resistant to flow variations; this more detailed analysis indicates that the most appropriate measure of disturbance may vary even among quite closely related taxa. The construction of a comprehensive theory of disturbance in streams requires that disturbance is quantified in a way that allows both multi-site and multi-study comparisons. The painted-particle approach, described here, has the potential to permit such standarized comparative studies.

Comparison of structural and functional approaches to determining landuse effects on grassland stream invertebrate communities

Abstract Effective catchment management in the face of landuse alteration depends on our ability to quantify ecologically significant changes and to discriminate among varying levels of impact. We compared the efficiency of traditional structural indices of change (species composition) with functional measures based on species traits (including life-history, trophic, and morphological features) in an analysis of grassland streams along a gradient of agricultural development (ungrazed native tussock, grazed tussock, extensively grazed pasture, and intensive dairy and deer farming). Streams were categorized in relation to overall agricultural intensity, and separately in terms of increasing nutrient concentrations and fine sediments on the streambed. Only 5 of 60 individual species demonstrated a significant separation across the landuse gradient, whereas 14 of 53 trait categories did so. Traits associated with population resilience (short generation time, asexual reproduction) became more prevalent with more intense agricultural pressure, reflecting predicted increases in intensity and frequency of stream disturbance. We observed a shift away from a tendency to lay unattached eggs at the water surface of the stream, reflecting the increasing likelihood of smothering by sediment, as well as increases in highly flexible and streamlined body shapes. Principal components and correspondence analyses involving species or trait composition all were able to discriminate landuse practises, but more of the overall between-landuse variance was accounted for by trait composition than species composition. All biological measures (species or trait composition) were correlated with both nutrient concentrations and sedimentation. Nutrient concentrations were better related to species and trait-category densities, whereas sedimentation was related to trait-category relative abundances. Overall, species traits successfully complemented traditional structural measures by helping to differentiate the consequences of landuse intensification in grassland stream communities. Rather than simply recording a loss or reduction of species, our functional approach was able to identify sensitive life-history characteristics linked to the functioning of ecosystems, thereby facilitating the development of targeted management actions.

Biological traits of stream macroinvertebrate communities: effects of microhabitat, reach, and basin filters

Abstract Stream invertebrate communities are the product of multiple-scale habitat filters, and a major goal in community ecology is to determine which scales most influence the relationships between habitat and community structure. We analyzed the relationships between habitat and the functional structure of invertebrate communities at 3 spatial scales (microhabitat, stream reach, basin), using 264 samples collected from 38 stream reaches in 2 basins in France. The habitat was described in terms of hydraulic conditions (Froude number), substrate size, and benthic particulate organic matter. The functional structure of the invertebrate communities was described using 60 categories of 12 biological traits. Relationships between habitat and traits were significant for 96 of 180 tests (r 2 ≤ 26%) at the microhabitat scale (within reaches). Relationships between habitat and traits were significant for 46 of 180 tests (r2 ≤ 34%) at the reach scale (within basins), and the effects of habitat variables on traits did not differ between the 2 basins. Invertebrate traits differed between basins in 34 of 60 trait categories (r2 ≤ 62%). Relationships between habitat and traits were consistent between the microhabitat and reach scales for all traits except body flexibility, number of reproductive cycles/y, and respiration patterns. At both scales, maximum size, body form, mode of attachment to the substrate, feeding habits, reproduction, lifespan, and strategies of dissemination were significantly correlated with habitat variables, especially hydraulics. These results illustrate adaptation to habitat characteristics in terms of resistance to drag and foraging strategies. However, overall differences between basins were inconsistent with patterns observed at smaller scales. In summary, the functional variability of invertebrate communities in stream reaches depended largely on microhabitat filters but also on other filters prevailing at the reach or larger scales.

Combining the fourth‐corner and the RLQ methods for assessing trait responses to environmental variation

Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples), and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait-nvironment relationships. Both methods are based on the analysis of the fourth-corner matrix, which crosses traits and environmental variables weighted by species abundances. However, they differ greatly in their outputs: RLQ is a multivariate technique that provides ordination scores to summarize the joint structure among the three tables, whereas the fourth-corner method mainly tests for individual trait-environment relationships (i.e., one trait and one environmental variable at a time). Here, we illustrate how the complementarity between these two methods can be exploited to promote new ecological knowledge and to improve the study of trait-environment relationships. After a short description of each method, we apply them to real ecological data to present their different outputs and provide hints about the gain resulting from their combined use.