Ecologically meaningful transformations for ordination of species data

Legendre, Pierre; Gallagher, Eugene D.

doi:10.1007/s004420100716

Cited by 4,311 publications

(3,021 citation statements)

References 20 publications

(22 reference statements)

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“…This transformation allows the use of Euclidian-based methods such as RDA rather than Chi-squared distance-based methods such as CCA for the analysis of species data. This option was recently suggested as a way to overcome a problem associated with the Chi-squared metric: that rare species may have a much larger influence on the analysis than common species [41]. Three quantitative environmental variables measured at the sampling sites (DWT, pH, and conductivity) were used as explanatory variables.…”

Section: S Cuspidatummentioning

confidence: 99%

The Ecology of Testate Amoebae (Protists) in Sphagnum in North-western Poland in Relation to Peatland Ecology

2005

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We studied the relationship between testate amoebae (Protozoa) communities and the depth to the water table (DWT), pH, conductivity, and microhabitat type in Sphagnum dominated peatlands of north-western Poland and built predictive (transfer function) models for inferring DWT and pH based on the testate amoebae community structure. Such models can be used for peatland monitoring and paleoecology. A total of 52 testate amoebae taxa were recorded. In a redundancy analysis, DWT and pH explained 20.1% of the variation in the species data and allowed us to identify three groups of taxa: species that are associated with (1) high DWT and low pH, (2) low DWT and low pH, and (3) high pH and mid-range DWT. Our transfer function models allow DWT and pH to be estimated with mean errors of 9.89 cm and 0.71 pH units. The prediction error of the DWT model and the tolerance of the species both increase with increasing dryness. This pattern mirrors the ecology of Sphagnum mosses: Species growing in wet habitats are more sensitive to change in water table depth than the species growing in drier microhabitats. Our results are consistent with studies of testate amoeba ecology in other regions, and they provide additional support for the use of these organisms in paleoecological and biomonitoring contexts. IntroductionTestate amoebae are unicellular organisms living in a variety of habitats including lakes and mires [3,32,65]. Sphagnum peatlands are characterized by a high diversity of microhabitats in which many testate amoebae species occur. Testate amoebae produce shells (tests) that can be proteinaceous, pseudochitinous, or agglutinated with one or two pseudostome(s) and are diagnostic for identification [70,77]. Testate amoebae are an important component in the soil microbial food web. Together with other protozoans, testate amoebae are believed to regulate bacterial populations [31] and to play a role in nutrient mineralization and plant growth [29]. Some species are mixotrophic and contain endosymbiotic algae [63].Many species have well-defined ecological preferences, and this stenotopy makes them very useful bioindicators [30,47]. Previous studies have shown that the abundance of each taxon and hence the structure of communities are controlled by a set of environmental variables. Water availability (moisture or water table depth) was often identified as being the single most important factor controlling testate amoebae community composition on peatlands, the second most important variable usually being pH [4-6, 10-12, 15, 21, 45, 46, 48, 49, 71, 76]. The correlation between testate amoebae communities and moisture conditions is increasingly used to infer palaeohydrological changes in peatlands and, in the case of ombrotrophic peatlands, these data are ultimately used to infer past climate changes [13, 16-19, 35, 44, 79]. In addition to paleoecology, testate amoebae research can be applied to environmental monitoring of natural ecosystems and those affected by human activities. Examples include the monitoring of lak...

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Section: S Cuspidatummentioning

confidence: 99%

The Ecology of Testate Amoebae (Protists) in Sphagnum in North-western Poland in Relation to Peatland Ecology

2005

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“…Hellinger transformed (Legendre and Gallagher, 2001) previously to being used as predictors in the analysis. variance of a factor that is independent of all previous factors.…”

Section: Resultsmentioning

confidence: 99%

“…Because trout and frog variables were binary, and to achieve more accurate R 2 in the model, these variables were standardized by Hellinger transformation (Legendre and Gallagher, 2001) before using them in FSO.…”

Section: (Multidimensional) Fuzzy Set Ordinationmentioning

confidence: 99%

Small lakes in big landscape: Multi-scale drivers of littoral ecosystem in alpine lakes

Zaharescu

Burghelea

Hooda

et al. 2016

Science of The Total Environment

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In low nutrient alpine lakes, the littoral zone is the most productive part of the ecosystem, and it is a biodiversity hotspot. It is not entirely clear how the scale and physical heterogeneity of surrounding catchment, its ecological composition, and larger landscape gradients work together to sustain littoral communities.A total of 113 alpine lakes from the central Pyrenees were surveyed to evaluate the functional connectivity between littoral zoobenthos and landscape physical and ecological elements at geographical, catchment and local scales, and to ascertain how they affect the formation of littoral communities. At each lake, the zoobenthic composition was assessed together with geolocation, catchment hydrodynamics, geomorphology and topography, riparian vegetation composition, the presence of trout and frogs, water pH and conductivity.Multidimensional fuzzy set models integrating benthic biota and environmental variables revealed that at geographical scale, longitude unexpectedly surpassed altitude and latitude in its effect on littoral ecosystem. This reflects a sharp transition between Atlantic and Mediterranean climates and suggests a potentially high horizontal vulnerability to climate change. Topography (controlling catchment type, snow coverage and lakes connectivity) was the most influential catchment-scale driver, followed by hydrodynamics (waterbody size, type and volume of inflow/outflow). Locally, riparian plant composition significantly related to littoral community structure, richness and diversity. These variables, directly and indirectly, create habitats for aquatic and terrestrial stages of invertebrates, and control nutrient and water cycles. Three benthic associations characterised distinct lakes. Vertebrate predation, water conductivity and pH had no major influence on littoral taxa.This work provides exhaustive information from relatively pristine sites, and unveils a strong connection between littoral ecosystem and catchment heterogeneity at scales beyond the local environment. This underpins the role of alpine lakes as sensors of local and large-scale environmental changes, which can be used in monitoring networks to evaluate further impacts.

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“…In addition, we transformed our matrix of relative amounts of compounds (originally in % of the total blend) with a Hellinger transformation, which is a relativization by row (sample unit) totals, followed by taking the square root of each element in the matrix, to make the floral scent data that contained many zero values (e.g., compounds absent in certain individuals, but present in others) suitable for multivariate analysis (Legendre & Gallagher, 2001; Legendre & Legendre, 1998). We then performed an analysis of similarities (ANOSIM) using the average Bray–Curtis distances among samples of the Hellinger‐transformed matrix and 1,000 permutations with the vegan package (version 2.0–5; (Oksanen et al., 2012)) in R to statistically test if the two Ophrys species differed in floral scent.…”

Section: Methodsmentioning

confidence: 99%

Floral scent and species divergence in a pair of sexually deceptive orchids

Gervasi

Selosse

Sauve

et al. 2017

Ecology and Evolution

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Speciation is typically accompanied by the formation of isolation barriers between lineages. Commonly, reproductive barriers are separated into pre‐ and post‐zygotic mechanisms that can evolve with different speed. In this study, we measured the strength of different reproductive barriers in two closely related, sympatric orchids of the Ophrys insectifera group, namely Ophrys insectifera and Ophrys aymoninii to infer possible mechanisms of speciation. We quantified pre‐ and post‐pollination barriers through observation of pollen flow, by performing artificial inter‐ and intraspecific crosses and analyzing scent bouquets. Additionally, we investigated differences in mycorrhizal fungi as a potential extrinsic factor of post‐zygotic isolation. Our results show that floral isolation mediated by the attraction of different pollinators acts apparently as the sole reproductive barrier between the two orchid species, with later‐acting intrinsic barriers seemingly absent. Also, the two orchids share most of their fungal mycorrhizal partners in sympatry, suggesting little or no importance of mycorrhizal symbiosis in reproductive isolation. Key traits underlying floral isolation were two alkenes and wax ester, present predominantly in the floral scent of O. aymoninii. These compounds, when applied to flowers of O. insectifera, triggered attraction and a copulation attempt of the bee pollinator of O. aymoninii and thus led to the (partial) breakdown of floral isolation. Based on our results, we suggest that adaptation to different pollinators, mediated by floral scent, underlies species isolation in this plant group. Pollinator switches may be promoted by low pollination success of individuals in dense patches of plants, an assumption that we also confirmed in our study.

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Ecologically meaningful transformations for ordination of species data

Cited by 4,311 publications

References 20 publications

The Ecology of Testate Amoebae (Protists) in Sphagnum in North-western Poland in Relation to Peatland Ecology

The Ecology of Testate Amoebae (Protists) in Sphagnum in North-western Poland in Relation to Peatland Ecology

Small lakes in big landscape: Multi-scale drivers of littoral ecosystem in alpine lakes

Floral scent and species divergence in a pair of sexually deceptive orchids

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