Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms

Abstract

International audience1. Diatoms include a great diversity of taxa and are recognized as powerful bioindicators of freshwater quality. However using diatoms for bioassess-ment is costly and time consuming, because most of the indices necessitate species-level identification. Simplifying diatoms-based assessment protocols has focused the attention of water-managers and researchers in recent years. 2. The increasing availability of genomic data and phylogenies can benefit in the development of bioassessment methods making use of these tools, where a clade plays the role of a species if relevant. Indeed, the null hypothesis is that closely related species are more likely to exhibit similar environmental sensitivity because of phylogenetic constraints and inheritance. Such patterns have been reported recently for sensitivity to a variety of pollutants for two important groups of bioindicators used for freshwater monitoring: benthic macroinvertebrates and diatoms. 3. We introduce a method to extract clusters of species sharing similar traits and being phylogenetically related. We apply this method on the general pollution sensitivity (IPS specific sensitivity value; Coste, 1982) of 262 species of diatoms and, by tuning the method settings; we generate different clade-based derivatives of the traditional IPS index. 4. Finally, we estimate traditional and derived IPS scores for 2119 natural communities of diatoms in eastern France to compare and assess the performances of these new indices. 5. Synthesis and applications. We show that phylogenetic approaches offer a scope for simplification without an important loss of information and we discuss the potential of their use in biomonitoring

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

“…The ecological guilds to which species belong (high-profile, low-profile, motile, euplanktonic) are given according to Rimet and Bouchez ( 30 ). Finally, the pollution sensitivity values and ecological weights of several diatom indices are given, such as the TDI (Trophic Diatom Index) ( 33 ), the TDI-Sweden, ( 34 ), the IPS (Pollution Sensitivity Index) ( 35 ) or the Phylogenetic-IPS ( 36 ).…”

Benthic Diatoms of the Ying River (Huaihe River Basin, China) and Their Application in Water Trophic Status Assessment

“…Diatoms include a great diversity of taxa, and researchers have been investigating simple and effective methods for their detection [49]. In our study, 370 species and varieties of diatoms were identified.…”

phylosignal: an R package to measure, test, and explore the phylogenetic signal

“…Finally, the function graphClust implements a simple method to perform traits clustering under phylogenetic constraints (Keck et al. In press a).…”

“…This dataset is deliberately kept simple for demonstration purposes: this is a very brief overview of the diversity existing in this clade but it constitutes a good case study (for a more comprehensive discussion about phylogenetic signal in diatoms sensitivity to pollutions, see Keck et al. In press a,b). The dataset is included in the package and can be loaded with the following command.…”