Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT.3D standardization

Abstract

1. Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. Biodiversity has at least three dimensions: (a) Taxonomic diversity (TD): a measure that is sensitive to the number and abundances of species. (b) Phylogenetic diversity (PD): a measure that incorporates not only species abundances but also species evolutionary histories. (c) Functional diversity (FD): a measure that considers not only species abundances but also species' traits.2. We integrate the three dimensions of diversity under a unified framework of Hill numbers and their generalizations. Our TD quantifies the effective number of equally abundant species, PD quantifies the effective total branch length, mean-PD (PD divided by tree depth) quantifies the effective number of equally divergent lineages, and FD quantifies the effective number of equally distinct virtual functional groups (or functional 'species'). Thus, TD, mean-PD and FD are all in the same units of species/lineage equivalents and can be meaningfully compared.3. Like species richness, empirical TD, PD and FD based on sampling data depend on sampling effort and sample completeness. For TD (Hill numbers), the iNEXT (interpolation and extrapolation) standardization was developed for standardizing sample size or sample completeness (as measured by sample coverage, the fraction of individuals that belong to the observed species) to make objective comparisons across studies. This paper extends the iNEXT method to the iNEXT.3D standardization to encompass all three dimensions of diversity via sample size-and sample coverage-based rarefaction and extrapolation under the unified framework. The asymptotic diversity estimates (i.e. sample size tends to infinity and sample coverage tends to unity) are also derived. In addition to individual-based abundance data, the proposed iNEXT.3D standardization is adapted to deal with incidencebased occurrence data. 4. We apply the integrative framework and the proposed iNEXT.3D standardization to measure temporal alpha-diversity changes for estuarine fish assemblage data spanning four decades. The influence of environmental drivers on diversity change are also assessed. Our analysis informs a mechanistic interpretation of 1927 Methods in Ecology and Evoluঞon CHAO et Al.

The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley

“…Methods to alleviate these problems have faced novel challenges with microbial data sets using high-throughput sequencing due to sequencing errors being indistinguishable from novel taxa ( Chiu & Chao, 2016 ). To alleviate these problems, species accumulation curves and estimated species richness were calculated with inext .3 d version 1.0.1, which extrapolates species richness based on individual sample sizes using unrarefied data ( Chao et al, 2014 , 2021 ; Hsieh et al, 2016 ). Confidence intervals in inext .3 d were calculated from 1,000 bootstrap replications.…”

Regional and local environment drive biogeographic patterns in intertidal microorganisms

“…Calculations were carried out using the R package 'iNEXT' 2.0.20. PD and FD are under the same unified Hill numbers framework as TD; thus, sampling effects were controlled for using standardization (Chao et al, 2021). The PD and FD metrics measure the effective number of phylogenetic and functional entitles in the community, which are defined as the mean branch length in the phylogenetic tree or the average of all Gower distances between species (Chao et al, 2021).…”

“…PD and FD are under the same unified Hill numbers framework as TD; thus, sampling effects were controlled for using standardization (Chao et al, 2021). The PD and FD metrics measure the effective number of phylogenetic and functional entitles in the community, which are defined as the mean branch length in the phylogenetic tree or the average of all Gower distances between species (Chao et al, 2021). The Gower dissimilarity matrix was used to represent functional distances and we calculated the asymptotic values for PD and FD using the online version of iNEXT 3D (https://chao.shiny apps.io/iNEXT_3D/).…”

Plasmodium falciparum Genetic Diversity in Coincident Human and Mosquito Hosts

“…(i) Population level. For the set of mosquito samples and the set of human samples, we calculated the population-level diversity of haplotypes, rarefaction curves, and population evenness using the R packages iNEXT.4steps v1.0.1 ( 10 ) and iNEXT.3D v1.0.1 ( 30 ).…”