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Recent developments in linear ordination methods in environmental sciences

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Sylvain Dolédec at Claude Bernard University Lyon 1
Sylvain Dolédec
D. Chessel
D. Chessel
D. Chessel
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Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
Dolédec, S., and D. Chessel. 1991. Recent developments in linear ordination methods for environmental sciences. Advances in
Ecology, India 1:133-155.
http://pbil.univ-lyon1.fr/R/articles/arti066.pdf
... [20,27,34,37] inter-classe et intra-classe des 199 relevés et 192 espèces sur les trois vallées. Cette méthode permet de traiter les données de composition spécifique des communautés comme de véritables données expérimentales en introduisant l'analyse de variance dans le domaine multivarié [12,27,33]. Nous avons donc étudié la structure végétation-vallée et la structure végétation-stade en éliminant successivement les différences inter-stade et inter-vallée au moyen des AFC «.conditionnelles.» ...
... La validité de la signification de la variabilité inter-vallée est testée par un test de permutation [23] de Monte-Carlo (2 000 permutations). Par la suite nous avons ordonnés les espèces endémiques Corso-Sarde et les espèces communes (non endémiques) de Corse, afin d'étudier la distribution des espèces endémiques et caractéristiques de chacune des vallées, sur le gradient écologique défini par les relevés (les espèces sont positionnées à la moyenne des stations où elles sont présentes) [12]. Les analyses ont été effectuées avec le logiciel ADE-4 [10,35] et l'effet conjoint des différentes vallées et stades dynamiques sur la richesse spécifique [14] a été analysé statistiquement grâce à un test ANOVA à un facteur effectuée avec le logiciel STATVIEW 5.0. ...
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... Between-group PCA calculates linear combinations of variables maximizing the between-group (in this case between species) variance instead of the overall variance. The inertia calculated in a between-group PCA represents the part of the total variance due to the differences between species [34]. ...
... To do this, we calculated the correlations between traits at the interspecific (axes discriminating species in the trait space) and intraspecific (axes discriminating individuals within species in the trait space) levels using both between-and within-PCA analyses. Within-group PCAs breakdown the structure within a group, in this case the group we used was species, by considering the data centred on species means [34]. To observe trait correlation within species, we also ran a PCA on individual data for each species. ...
Leaf trait variability between and within subalpine grassland species differs depending on site conditions and herbivory
Article
Full-text available
  • Jul 2019
Plant traits are commonly used to predict ecosystem-level processes, but the validity of such predictions is dependent on the assumption that trait variability between species is greater than trait variability within a species-the robustness assumption. Here, we compare leaf trait intraspecific and interspecific variability depending on geographical differences between sites and 5 years of experimental herbivore exclusion in two vegetation types of subalpine grasslands in Switzerland. Four leaf traits were measured from eight herbaceous species common to all 18 sites. Intraspecific trait variability differed significantly depending on site and herbivory. However, the amount and structure of variability depended on the trait measured and whether considering leaf traits separately or multiple leaf traits simultaneously. Leaf phosphorus concentration showed the highest intraspecific variability, while specific leaf area showed the highest interspecific variability and displayed intraspecific variability only in response to herbivore exclusion. Species identity based on multiple traits was not predictable. We find intraspecific variability is an essential consideration when using plant functional traits as a common currency not just species mean traits. This is particularly true for leaf nutrient concentrations, which showed high intraspecific variability in response to site differences and herbivore exclusion, a finding which suggests that the robustness assumption does not always hold.
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... where analyze data about the floristic composition of the plots, but they can also be complementary: while PCA highlights the abundant species, CA highlights rare species (Hill, 1973, in Dolédec & Chessel, 1991 and focuses on community composition rather than species abundance (Dolédec & Chessel, 1991). These multivariate analyses were followed by between-class analysis with habitat type as class. ...
... where analyze data about the floristic composition of the plots, but they can also be complementary: while PCA highlights the abundant species, CA highlights rare species (Hill, 1973, in Dolédec & Chessel, 1991 and focuses on community composition rather than species abundance (Dolédec & Chessel, 1991). These multivariate analyses were followed by between-class analysis with habitat type as class. ...
Soil seed banks in the floodplain of a large river: A test of hypotheses on seed bank composition in relation to flooding and established vegetation
Article
  • May 2019
Questions This study investigates soil seed banks in relation to established vegetation in the floodplain of a large river with high energy floods. It addresses the composition of seed banks and extant vegetation over a wide flooding and succession gradient. Tested hypotheses were: (i) species richness and seed bank density are highest in mid‐succession habitats, (ii) seed bank variability increases with succession, (iii) the proportion of species in the established vegetation with permanent seed banks decline with succession, (iv) similarity between vegetation and seed bank declines with succession. Location Mareau‐aux‐Prés, the Loire River, close to Orléans, France. Methods Seed banks and vegetation were sampled in five habitats from a succession series: (1) Pioneer vegetation of shores and sandbanks, (2) softwood shrubs, (3) softwood forest, (4) mature forest, (5) Elytrigia‐dominated grasslands. Sample units were 5m x 5m plots. Soil samples were taken from the upper 6 cm. Seed banks were studied via the seedling emergence method, followed by screening of sediment for remaining seeds. Composition of seed banks was compared to that of vegetation using the Sørenson similarity index. Results Seed bank density varied between 260 and 11260 seeds.m‐². Clear differences between habitats existed in the composition of species in seed banks and established vegetation. Seeds of most dominant species were distributed across the whole range of floodplain habitats but were more restricted in the vegetation. Species richness and seed bank densities did not vary with succession as expected, but the proportion of species that produce persistent seed banks did decline with sucession. Conclusions Floodplains of large rivers provide an excellent context to test hypotheses about the processes that influence the links between seed banks and standing vegetation. In the case of high‐energy floods and high sediment dynamics, the methods commonly used to study seed banks can however be questioned. This article is protected by copyright. All rights reserved.
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... To decompose the part of the total variance due to the differences between guilds, we used between-PCA on the nine traits [22]. As the number of species differed among fish guilds, we used a re-sampling procedure to balance the datasets (i.e., equal numbers of species) and then sub-sampled the original dataset by drawing randomly from 1000 balanced data subsets containing the smallest number of species per guild [23]. ...
Do Morphological Traits Predict Ecological Guilds of the Mekong Fish Fauna?
Article
Full-text available
  • Jul 2021
Southeast Asian riverine fishes are classified into three guilds (‘black’, ‘white’ and ‘grey’ species) based on their reproductive and migration strategies. In this study, we aimed to investigate whether fish morphology could be used to predict the Mekong fish guilds. Nine dimensionless ratios of fish morphological traits were used to describe the locomotion and food acquisition strategies of 121 fish species. The links between morphological traits and fish guilds were assessed using a principal component analysis (PCA) and a variance partitioning analysis, which revealed a strong morphological overlap between the guilds. Despite the high contribution of intra-guild variability to overall morphological variability (~90%), black and white fish significantly differed in terms of locomotion-related traits. Mekong fish guilds were satisfactorily predicted by using a random forest (RF) model, which produced a percentage of successful classification of ca 50% for each of the three guilds. Caudal propulsion efficiency, pectoral fin vertical position and body elongation were the most significant traits in the RF predictive model. Although the present study provides initial insight into the links between Mekong fish morphology and ecological guilds, further research is needed in order to clarify the relationship between species morphology, migratory status and responses to environmental variation.
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... * Une ACP centrée a été réalisée sur les données faunistiques recueillies en milieu lotique sur les 38 stations prospectées au cours des 4 campagnes d'échantillonnage. En effet, ce type d'analyse peut être appliqué aux données faunistiques quand les surfaces échantillonnées sont connues (Dolédec & Chessel, 1991). Préalablement, les taxons rares (dont le nombre d'occurrences fut inférieur à 4 sur l'ensemble des prélèvements) furent éliminés de l'analyse de même que les Insectes indéterminés. ...
Caractérisations physico-chimique et biologique des cours d'eau de la Nouvelle-Calédonie. Proposition d'un indice biotique fondé sur l'étude des macroinvertébrés benthiques
Thesis
  • May 1999
Forty-one stations located on 14 rivers spread over the whole of New Caledonia were periodically sampled from October 1996 to October 1997. Benthic invertebrate samples were taken at each of the stations, then identified and counted in the laboratory. . At the same time, water samples were analyzed at each study station. The physico-chemical nature of the waters of the rivers of the mainland is strongly influenced by the drained geological substrates. Organic pollution is generally not very significant in the territory, the highest concentrations of nitrates, ammonium and organic matter are measured in the rivers located near certain villages, tribes or towns, in the agglomeration of noumea and level of the lower courses of the rivers of the west coast. A physico-chemical typology of the study stations based on their geographic location, land use and the geological nature of the rocks was highlighted using multivariate analyzes. The benthic macrofauna of rivers is dominated by insects. The environments most conducive to the development of benthic macrofauna and which present the maximum specific diversity are forest streams. In contrast, the watercourses draining altered peridotites and far from any human occupation are characterized by less diversified and less abundant benthic populations due to their low organic matter content. In addition, some taxa show a generic and specific endemism linked to the peridotitic substrate like terrestrial insects. A biotypology of the study stations has been defined, based on the same criteria as those of the physico-chemical typology. Land use, riverine vegetation and the geological nature of watersheds represent the main factors explaining the distribution and distribution of benthic macrofauna in rivers. An original biotic index specific to the rivers of New Caledonia is proposed in this work. The biotic index of new caledonia (ibnc) makes it possible to detect organic pollution in current environments. It refers to 62 frequent and easily identifiable taxa which have been assigned a score according to their sensitivity to organic matter.
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... Between-group factorial correspondence analyses (Dolédec & Chessel, 1991) were conducted to investigate the influence of survey (two different sampling dates: February and March 2015) and habitats (healthy vs. degraded) on the variability of the species composition of cyanobacterial assemblages. Between-group correspondence analyses uses groups (i.e., categorical factor, e.g., stations) as instrumental variables (e.g., to test the between-stations variability of cyanobacterial assemblages composition). ...
Benthic cyanobacteria on coral reefs of Moorea Island (French Polynesia): diversity response to habitat quality
Article
Full-text available
  • Oct 2019
  • HYDROBIOLOGIA
The marine benthic cyanobacteria on coral reefs of Moorea Island (French Polynesia) show significant changes in species diversity in response to environmental impacts. To study these changes in cyanobacterial diversity, we examined pristine and degraded coral reefs by combining microscopy of morphological properties of the taxa with characterization of each by 16S rRNA gene sequences. A total of 30 cyanobacterial species have been recorded, of which 10 (33%) of them represent a new record for Moorea Island. The majority of morpho-species we identified could be distinguished by phylogenetic analyses of 61 sequences. Our survey results showed a sharp distinction in the composition of benthic cyanobacterial assemblages from healthy (high living coral cover) versus degraded habitats (low live coral cover due to anthropogenic activities). Finally, 21 bloom-forming species were identified, occurring mostly in environmentally impacted area (north coast). Blooms were dominated by three species: Anabaena sp.1, Hydrocoleum majus-B, Lyngbya majuscula. This study provides novel insights into the taxonomy of tropical benthic cyanobacteria as important environmental indicators and advocates the use of new bioevaluative tools for the management of coral reef environments.
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Comparison of structural and functional approaches to determining landuse effects on grassland stream invertebrate communities
Article
  • Mar 2006
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.
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Suivi de la qualité bactériologique des eaux de surface du Maroc orientalMonitoring the bacteriological quality of surface water in Eastern Morocco
Article
  • Jan 2019
L’oued de la Moulouya et ses affluents demeurent les principales ressources en eau pour irriguer les champs agricoles avoisinants de la région de Berkane qui représentent l’activité principale de cette région. L’évaluation de la qualité des eaux de ces ressources s’avère une nécessité pour maintenir leur bon fonctionnement et par la suite assurer un bon rendement des produits agricoles. Pour ce faire, un suivi mensuel de prélèvements des eaux a été réalisé dans l’oued de la Moulouya et son affluent Zegzel-Cherâa durant une année de décembre 2015 à novembre 2016. Ces prélèvements ont fait l’objet d’analyses bactériologiques selon les protocoles décrits par les normes marocaines ISO et les recommandations de l’Organisation mondiale de la santé (OMS). Les analyses bactériologiques ont montré que l’oued de Cherâa est soumis à une forte pollution d’origine humaine et animale, avec une prédominance de la source humaine. En effet, la charge bactérienne (coliformes totaux [CT], coliformes fécaux [CF], Escherichia coli [EC], streptocoques fécaux [SF], etc.) est supérieure aux normes marocaines du Secrétariat d’État auprès du ministère de l’Énergie, des Mines, de l’Eau et de l’Environnement (SEEE, 2007) indiquant ainsi que les eaux sont de mauvaise qualité. L’analyse explicative (ACPn) réalisée sur les variables étudiées a permis de mettre en évidence un gradient de pollution pour l’oued Cherâa et a également fait ressortir l’automne comme la saison la plus chargée en bactéries indicatrices de pollution. L’abondance de ces microorganismes dans les cours d’eau traduit la présence possible de bactéries pathogènes qui pourraient causer des maladies au sein de la population qui utilise ces eaux pour boire et pour l’irrigation. Les eaux de l’oued Cherâa sont impropres à la consommation.
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Effect of physicochemical and microbiological parameters on the water quality of wadi Zegzel
Article
  • Jan 2019
Wadi Zegzel is a mountain stream inside a site of ecological and biological interest (SIBE) in the Northeast of Morocco. The impact of various anthropogenic activities (agricultural, tourism ...) was obvious. It is suggested that surveillance of Wadi Zegzel is necessary for the proper management and preservation of this heritage. Normed Principal Component Analysis (PCA) was applied to standardize the data to evaluate correlations between physicochemical variables (T ° C, pH, BOD5, COD, NH4 ...) and microbiological variables (FTMA, TC, FC, EC, SF ...) and their spatiotemporal structure (the spatial effect and the seasonal effect).The upstream Zegzel is characterized by a gradient of mineralization in winter and it’s downstream by a gradient of faecal pollution during the summer. The waters of the WadiZegzel are below the limit of Moroccan standards for the quality of surface water and water intended for irrigation. Therefore, they are considered of good quality for agricultural uses.
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