Canonical Ordination

2010 ◽  
pp. 153-225 ◽  
Author(s):  
Daniel Borcard ◽  
François Gillet ◽  
Pierre Legendre
Keyword(s):  
Zootaxa ◽  
2007 ◽  
Vol 1600 (1) ◽  
pp. 1-175 ◽  
Author(s):  
M. FLORENCIA VERA CANDIOTI

I studied anatomy, gut content, and the relationship among these traits in a set of anuran tadpoles. Larval stages (mainly Gosner stages 31–36) of nineteen species from various lentic environments were selected. Morphological characters from the skeleton, musculature, oral apparatus and buccopharyngeal cavity were recorded, and a gut content analysis was performed, with emphasis on food size distribution. Ordination techniques were applied in order to find patterns of similarity in morphology and gut content. Canonical ordination methods were used to investigate the relationship among gut content, morphology, and phylogeny in the species considered. The results show that several skeletal, muscular, and buccal characters are relatively maintained within genera. Other features, which have appeared independently in different lineages, reflect convergence phenomena in some cases related to ecological aspects. The configuration of the hyobranchial skeleton, the development of the buccal floor depressor and levator muscles, and mouth gape width correlate with prey size. In some species, morphology is clearly related with feeding. Tadpoles that ingest large food particles relative to their body length present morphological traits attributable to macrophagy. Taxonomically unrelated tadpoles of Dendropsophus nanus, D. microcephalus and Ceratophrys cranwelli possess hyobranchial skeletons with robust, rostrocaudally long ceratohyals and reduced branchial baskets with short ceratobranchials devoid of lateral projections and spicules. Lepidobatrachus llanensis tadpoles have laterally extended ceratohyals which, along with the lateral extension of the jaws, result in a very wide oral apparatus and an ample buccopharyngeal cavity that allows the tadpole to ingest large and whole prey; the branchial basket, although its ceratobranchials lack lateral projections and spicules, is slightly reduced in area. The four species mentioned have a noticeable development of the buccal floor depressor muscles, and buccal cavities with scarce filtering and entrapping structures. In Elachistocleis bicolor, Dermatonotus muelleri, Chiasmocleis panamensis, and Xenopus laevis tadpoles, the branchial basket occupies >70% of the total hyobranchial skeleton area, and the hypobranchial plates are highly reduced; the buccal floor levator muscles are well-developed, with an increased site of attachment on the ventral expansion of the lateral process of the ceratohyal; the scarcity of the filtering structures in the buccopharyngeal cavity are balanced with the great development of the branchial filters and secretory zones; all these features relate to a diet based on small particles not significantly different from those of most other species; however, experimental studies show that species with similar hyobranchial apparatus and muscles are the most efficient when retaining minute particles. Finally, a large group of species present generalized morphological characters, such as a branchial basket occupying about 50% of the total hyobranchial apparatus, intermediate values of mouth gape width and buccal floor levator / depressor muscles ratio, and abundant filtering structures in the buccopharyngeal cavity; these species feed frequently on food particles between 1–30% of the tadpole body length; however, in some of the species, macrophagous diets are also reported in the literature, indicating that this morphology is flexible in more ample prey size ranges.


Geoderma ◽  
1991 ◽  
Vol 49 (1-2) ◽  
pp. 1-32 ◽  
Author(s):  
I.O.A. Odeh ◽  
D.J. Chittleborough ◽  
A.B. McBratney

2020 ◽  
Vol 12 (24) ◽  
pp. 10473
Author(s):  
Peace Liz Sasha Musonge ◽  
Pieter Boets ◽  
Koen Lock ◽  
Minar Naomi Damanik Ambarita ◽  
Marie Anne Eurie Forio ◽  
...  

The Rwenzori region in Uganda, a global biodiversity hotspot, is currently undergoing exponential economic and population growth, which puts continuous stress on its freshwater ecosystems. In Sub-Saharan Africa, biomonitoring campaigns using region-specific biotic indices is limited, particularly in Uganda. In this research, we present the Rwenzori Score (RS), a new macroinvertebrate-based biotic index developed to specifically assess the aquatic health of Rwenzori streams and rivers. We collected and measured both biological and physicochemical variables and identified 34,202 macroinvertebrates, belonging to 64 different taxa. The RS was developed in two steps. First, using canonical ordination, we identified chemical variables that correlated significantly with gradients in macroinvertebrate assemblage distribution and diversity. Second, based on selected variables and weighted averages, we determined specific family indicator values and assigned pollution tolerance values (varying from 1: tolerant; to 10: sensitive) to a family. Finally, we established four water quality classes: poor, fair, good, and excellent. The RS is highly correlated with the Average Score Per Taxon System (p < 0.05), a well-known and widely used biotic index. The RS has 5 unique taxa that are not included in other regional indices. In this regard, the development of the RS is a beneficial tool for tailor-made biomonitoring that can contribute to the sustainable development of the Rwenzori stream and river basins.


2014 ◽  
Vol 281 (1778) ◽  
pp. 20132728 ◽  
Author(s):  
Pierre Legendre ◽  
Olivier Gauthier

This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran's eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.


2009 ◽  
Vol 75 (22) ◽  
pp. 7006-7016 ◽  
Author(s):  
Robert Pieper ◽  
J�r�me Bindelle ◽  
Brian Rossnagel ◽  
Andrew Van Kessel ◽  
Pascal Leterme

ABSTRACT The influence of the carbohydrate (CHO) composition of cereal cultivars on microbial ecophysiology was studied using an in vitro model of the porcine gastrointestinal tract. Ten hull-less barley cultivars, six barley cultivars with hulls, six oat cultivars, and six oat groats that differed in β-glucan, nonstarch polysaccharide (NSP), and starch contents and starch type were hydrolyzed enzymatically and incubated for 72 h with pig feces. Fermentation kinetics were modeled, and microbial compositions and short-chain fatty acid (SCFA) profiles were analyzed using terminal restriction fragment length polymorphism and gas chromatography. Cluster analysis and canonical ordination revealed different effects on fermentation and microbial ecology depending on the type of CHO and cultivar. First, in cultivars of barley with hulls and oats, the cellulose and insoluble NSP contents (i) increased Ruminococcus flavefaciens-like and Clostridium xylanolyticum-like phylotypes, (ii) increased acetate production, and (iii) decreased fermentation activity. Second, in hull-less barley cultivars the β-glucan, amylose, amylopectin, crude protein, and soluble NSP contents determined the microbial community composition and activity as follows: (i) the amylose contents of the hull-less barley varieties increased the butyrate production and the abundance of Clostridium butyricum-like phylotypes, (ii) the β-glucan content determined the total amounts of SCFA, and (iii) the amylopectin and starch contents affected the abundance of Clostridium ramosum-like phylotypes, members of Clostridium cluster XIVa, and Bacteroides-like bacteria. Finally, the effect of CHO on proliferation of Salmonella enterica in the model was determined. Salmonella cell counts were not affected, but the relative proportion of Salmonella decreased with hull-less barley cultivars and increased with oat cultivars as revealed by quantitative PCR. Our results shed light on the complex interactions of cereal CHO with intestinal bacterial ecophysiology and the possible impact on host health.


2012 ◽  
Vol 7 (4) ◽  
pp. 731-740 ◽  
Author(s):  
Iga Lewin ◽  
Krzysztof Szoszkiewicz

AbstractThe ecological drivers of macrophyte development in a lowland agricultural area were tested based on a 2008 survey on the Wkra River catchment. Our survey was carried out in the rivers of an agricultural area with relatively high concentrations of both nitrates and phosphates in the water. By using the Polish macrophyte method, we were able to calculate several botanical metrics. Canonical ordination analyses used to relate biological data to environmental variables such as physical and chemical parameters of water, surface water velocity or river width, were carried out using CANOCO for Windows. Redundancy analysis (RDA) showed that pH and alkalinity were the parameters best correlated with the distribution of macrophytes and values of macrophyte indices. The recorded values of the Macrophyte Index for River in the Wkra River and its tributaries reflected their good and moderate ecological status (the Water Framework Directive scale). Despite the fact that nutrient concentrations in the water were relatively high and that most of the sites represented eutrophic conditions, the results of this survey showed that non-nutrient parameters may play an important role in explaining aquatic plant occurrence in rivers that have been subjected to eutrophication.


2006 ◽  
Vol 22 (6) ◽  
pp. 705-717 ◽  
Author(s):  
Ana-Maria Benavides ◽  
Jan H. D. Wolf ◽  
Joost F. Duivenvoorden

The species richness, number of plants, biomass, and species composition of holo- and hemi-epiphytes were recorded in fifty-six 0.04-ha plots, distributed over forest fallows of 2–30 y old and mature forests in lowland Amazonia (Amacayacu National Park, Colombia). A total of 9190 epiphytic plants representing 162 species were recorded on 4277 phorophytes. Seventy species were classified as holo-epiphyte and 85 as hemi-epiphyte. Aroids were most diverse (58 species) and represented 76% of the total recorded biomass. Anemochory was more dominant among holo-epiphytes and zoochory among hemi-epiphytes. The species richness, density and biomass of both holo- and hemi-epiphytes increased significantly from young fallows to old fallows and mature forests. Hemi-epiphytes had greater density and biomass than holo-epiphytes. In canonical ordination, forest age did not relate to the species composition of holo-epiphytes. However, for hemi-epiphytes, the age effect was significant, suggesting that species turnover takes place in the ageing fallows.


2008 ◽  
Vol 36 (1-2) ◽  
Author(s):  
Hortência Maria Pereira ARAUJO ◽  
Viviane RIBEIRO

The purpose of this work was to study the composition and abundance of the mesozooplankton at two stations at the continental shelf off Sergipe. At each station, oblique plankton tows were carried using plankton nets with 200 µm mesh size, in six hours intervals during three consecutive days. One hundred and three taxa were identified and Copepoda was the dominant group with fifty one species. The mesozooplankton assemblage was composed by coastal, neritic and oceanic tropical species. There were significant differences in composition and abundance between the two studied stations (p<0,05) but not between tidal stages. At station 1, the most abundant species were Creseis acicula, Oikopleura spp., Temora stylifera, Paracalanus quasimodo and Aglaura hemistoma, and at station 2 Paracalanus quasimodo, Paracalanus spp., Siphonophora, Gastropoda and Decapoda larvae. Coastal species such as Parvocalanus crassirostris, Acartia lilljeborgi, Euterpina acutifrons and Corycaeus giesbrechti occurred only at the last station, located close to the mouth of the São Francisco River, where surface salinity and transparency values were low. In this station the salinity average value at surface was 30,8±1,9 and at the bottom layer was 35.0±0.3 PSU. Mesozooplanhton density values ranged between 124 ind.m-3 and 2,658 ind.m-3 at station 1, and from 734 ind.m-3 to 3,061 ind.m-3 at station 2. A Monte Carlo test based on a canonical ordination revelead that local depth and water transparency were significantly correlated to the mesozooplankton distribution. Key words: zooplankton community, Copepoda, shelf off Sergipe, tropical.


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