Ecoindicators: An R Package for the Identification of Indicator Taxonomic Units

Andrés Esteban Duhour; Hernán de la Vega; Liliana Falco; Carlos Coviella; Nicolás Velazco; Rosana Sandler; Macarena Rionda; Mónica Díaz Porres; Leonardo Saravia

doi:10.5334/jors.452

Ecoindicators: An R Package for the Identification of Indicator Taxonomic Units

Volume 11 (2023): Issue 1

By: Andrés Esteban Duhour , Hernán de la Vega , Liliana Falco , Carlos Coviella , Nicolás Velazco , Rosana Sandler , Macarena Rionda , Mónica Díaz Porres and Leonardo Saravia

Open Access

|Oct 2023

Abstract

The sensitivity of some taxonomic groups to environmental conditions allows for their use as ecological state indicators. In ecological communities, this analysis is of interest to know which species or taxa are indicators of particular environment conditions, taking into account their presence in a set of sampling units.

There are different approaches to estimate indicator species, in this work we develop a new tool for this task identifying indicator units defined as species (or taxa) whose observed frequencies are not uniform between environments or groups of sample units. The package provides methods to estimate the indicator species, the belonging of new samples to a given environment, and returns the frequency of taxonomic units in a selected combination of environmental factors as an estimation of the ecological niche. EcoIndicators was tested on a data set provided with the package and on independent samples of soil fauna communities and is freely available in https://github.com/lsaravia/EcoIndicators.

References

Bedano JC, Domínguez A, Arolfo, R. Assessment of soil biological degradation using mesofauna. Soil and Tillage Research. 2011; 117: 55–60. DOI: 10.1016/j.still.2011.08.007
Open DOI Search in Google Scholar Back to article
Chytrý M, Tichý L, Holt J, Botta-Dukát Z. Determination of diagnostic species with statistical fidelity measures. Journal of Vegetation Science. 2002; 13: 79–90. DOI: 10.1111/j.1654-1103.2002.tb02025.x
Open DOI Search in Google Scholar Back to article
De Cáceres M, Legendre P. Associations between species and groups of sites: indices and statistical inference. Ecology. 2009; 90: 3566–3574. DOI: 10.1890/08-1823.1
Open DOI Search in Google Scholar Back to article
De Cáceres M, Legendre P, Wiser SK, Brotons L. Using species combinations in indicator value analyses. Methods in Ecology and Evolution. 2012; 973–982. DOI: 10.1111/j.2041-210X.2012.00246.x
Open DOI Search in Google Scholar Back to article
de la Vega H, Falco L, Saravia L, Sandler R, Duhour A, Coviella C. EcoIndicators; 2019. DOI: 10.5281/zenodo.5772829
Open DOI Search in Google Scholar Back to article
de la Vega H, Falco L, Saravia L, Sandler R, Duhour A, Velazco VN, Coviella C. An algorithm for the identification of indicator taxonomic units and their use in analyses of ecosystem state. Revista de Modelamiento Matemático de Sistemas Biológicos. 2022; 2: 1–10. URL: https://revistammsb.utem.cl/?p=437. DOI: 10.1101/2022.05.16.492087
Open DOI Search in Google Scholar Back to article
Dufrêne M, Legendre P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs. 1997; 67: 345–366. DOI: 10.1890/0012-9615(1997)067[0345:SAAIST]2.0.CO;2
Open DOI Search in Google Scholar Back to article
George PB, Keith AM, Creer S, Barrett GL, Lebron I, Emmett BA, Robinson DA, Jones DL. Evaluation of mesofauna communities as soil quality indicators in a national-level monitoring programme. Soil Biology and Biochemistry. 2017; 115: 537–546. DOI: 10.1016/j.soilbio.2017.09.022
Open DOI Search in Google Scholar Back to article
Guerra CA, Bardgett RD, Caon L, Crowther TW, Delgado-Baquerizo M, Montanarella L, Navarro LM, Orgiazzi A, Singh, BK, Tedersoo L, Vargas-Rojas, R, Briones MJI, Buscot F, Cameron EK, Cesarz S, Chatzinotas A, Cowan DA, Djukic I, van den Hoogen J, Lehmann A, Maestre FT, Marín C, Reitz T, Rillig MC, Smith LC, de Vries FT, Weigelt A, Wall DH, Eisenhauer N. Tracking, targeting, and conserving soil biodiversity. Science. 2021; 371(6526): 239–241 DOI: 10.1126/science.abd7926
Open DOI Search in Google Scholar Back to article
El Mujtar V, Muñoz N, Prack Mc Cormick B, Pulleman M, Tittonell P. Role and management of soil biodiversity for food security and nutrition; where do we stand? Global Food Security. 2019; 20: 132–144. DOI: 10.1016/j.gfs.2019.01.007
Open DOI Search in Google Scholar Back to article
Ooms A, Dias A, van Oosten A, Cornelissen J, Ellers J, Berg M. Species richness and functional diversity of isopod communities vary across an urbanisation gradient, but the direction and strength depend on soil type Soil Biology and Biochemistry. 2020; 148: 107851. DOI: 10.1016/j.soilbio.2020.107851
Open DOI Search in Google Scholar Back to article
Ricotta C, Carboni M, Acosta AT, Mason NN. (ed.) Let the concept of indicator species be functional! Journal of Vegetation Science, Wiley. 2015; 26: 839–847. DOI: 10.1111/jvs.12291
Open DOI Search in Google Scholar Back to article
Ricotta C, Pavoine S, Cerabolini BEL, Pillar VD. A new method for indicator species analysis in the framework of multivariate analysis of variance. Methods In Vegetation Science. 2021; 32(2): e13013. DOI: 10.1111/jvs.13013
Open DOI Search in Google Scholar Back to article
Roberts DW. labdsv: Ordination and Multivariate Analysis for Ecology. R package. version 2.0-1; 2019. https://CRAN.R-project.org/package=labdsv.
Search in Google Scholar Back to article
Rocha L, Hegoburu C, Torremorell A, Feijoó C, Navarro E, Fernández H. Use of ecosystem health indicators for assessing anthropogenic impacts on freshwaters in Argentina: a review. Environmental Monitoring and Assessment. 2020; 192: 611. DOI: 10.1007/s10661-020-08559-w
Open DOI Search in Google Scholar Back to article
Sandler RV. Indicadores de sustentabilidad del suelo basados en la estructura y funcionamiento de la fauna edáfica. Ph.D. dissertation. Universidad Nacional de General Sarmiento. Argentina; 2019. URL: http://repositorio.ungs.edu.ar:8080/xmlui/handle/UNGS/728.
Search in Google Scholar Back to article

Articles in this issue

DOI: https://doi.org/10.5334/jors.452 | Journal eISSN: 2049-9647

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Language: English

Submitted on: Dec 30, 2022

Accepted on: Aug 29, 2023

Published on: Oct 13, 2023

Published by: Ubiquity Press

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

Keywords:

Indicator species,

ecological community analysis,

samples grouping estimation,

ecological niche,

soil fauna

© 2023 Andrés Esteban Duhour, Hernán de la Vega, Liliana Falco, Carlos Coviella, Nicolás Velazco, Rosana Sandler, Macarena Rionda, Mónica Díaz Porres, Leonardo Saravia, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 11 (2023): Issue 1