A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data

J. Podaní, Sandrine Pavoine, Carlo Ricotta

Research output: Contribution to journalArticle

Abstract

Community structure as summarized by presence-absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits-a more or less subjective element of the framework-remains to be investigated.

Original languageEnglish
Article number250
JournalMathematics
Volume6
Issue number11
DOIs
Publication statusPublished - Nov 12 2018

Fingerprint

Community Structure
Phylogenetics
Dissimilarity
Redundancy
Point Cloud
Coefficient
Vegetation
Centroid
Framework
Ternary
Exception
Replacement
Excess
Express
Diagram
Numerical Results
Decrease
Evaluation

Keywords

  • Beta diversity
  • Diversity partitioning
  • Jaccard dissimilarity
  • Redundancy
  • Richness difference
  • Simplex plot
  • Species replacement

ASJC Scopus subject areas

  • Mathematics(all)

Cite this

A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data. / Podaní, J.; Pavoine, Sandrine; Ricotta, Carlo.

In: Mathematics, Vol. 6, No. 11, 250, 12.11.2018.

Research output: Contribution to journalArticle

@article{51966210e94343999a381db4f1493b25,
title = "A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data",
abstract = "Community structure as summarized by presence-absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits-a more or less subjective element of the framework-remains to be investigated.",
keywords = "Beta diversity, Diversity partitioning, Jaccard dissimilarity, Redundancy, Richness difference, Simplex plot, Species replacement",
author = "J. Podan{\'i} and Sandrine Pavoine and Carlo Ricotta",
year = "2018",
month = "11",
day = "12",
doi = "10.3390/math6110250",
language = "English",
volume = "6",
journal = "Mathematics",
issn = "2227-7390",
publisher = "MDPI AG",
number = "11",

}

TY - JOUR

T1 - A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data

AU - Podaní, J.

AU - Pavoine, Sandrine

AU - Ricotta, Carlo

PY - 2018/11/12

Y1 - 2018/11/12

N2 - Community structure as summarized by presence-absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits-a more or less subjective element of the framework-remains to be investigated.

AB - Community structure as summarized by presence-absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits-a more or less subjective element of the framework-remains to be investigated.

KW - Beta diversity

KW - Diversity partitioning

KW - Jaccard dissimilarity

KW - Redundancy

KW - Richness difference

KW - Simplex plot

KW - Species replacement

UR - http://www.scopus.com/inward/record.url?scp=85057016272&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85057016272&partnerID=8YFLogxK

U2 - 10.3390/math6110250

DO - 10.3390/math6110250

M3 - Article

AN - SCOPUS:85057016272

VL - 6

JO - Mathematics

JF - Mathematics

SN - 2227-7390

IS - 11

M1 - 250

ER -