Drivers of microbiome biodiversity: a review of general rules, feces, and ignorance

AT Reese, RR Dunn - MBio, 2018 - Am Soc Microbiol
The alpha diversity of ecologic communities is affected by many biotic and abiotic drivers
and, in turn, affects ecosystem functioning. Yet, patterns of alpha diversity in host-associated …

Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through Hill numbers

A Chao, CH Chiu, L Jost - Annual review of ecology, evolution …, 2014 - annualreviews.org
Hill numbers or the effective number of species are increasingly used to quantify species
diversity of an assemblage. Hill numbers were recently extended to phylogenetic diversity …

Sampling biases shape our view of the natural world

AC Hughes, MC Orr, K Ma, MJ Costello, J Waller… - …, 2021 - Wiley Online Library
Spatial patterns of biodiversity are inextricably linked to their collection methods, yet no
synthesis of bias patterns or their consequences exists. As such, views of organismal …

The number of tree species on Earth

R Cazzolla Gatti, PB Reich… - Proceedings of the …, 2022 - National Acad Sciences
One of the most fundamental questions in ecology is how many species inhabit the Earth.
However, due to massive logistical and financial challenges and taxonomic difficulties …

[HTML][HTML] The gut virome database reveals age-dependent patterns of virome diversity in the human gut

AC Gregory, O Zablocki, AA Zayed, A Howell… - Cell host & …, 2020 - cell.com
The gut microbiome profoundly affects human health and disease, and their infecting viruses
are likely as important, but often missed because of reference database limitations. Here, we …

Quantifying sample completeness and comparing diversities among assemblages

A Chao, Y Kubota, D Zelený, CH Chiu, CF Li… - Ecological …, 2020 - Wiley Online Library
We develop a novel class of measures to quantify sample completeness of a biological
survey. The class of measures is parameterized by an order q≥ 0 to control for sensitivity to …

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

A Chao, NJ Gotelli, TC Hsieh, EL Sander… - Ecological …, 2014 - Wiley Online Library
Quantifying and assessing changes in biological diversity are central aspects of many
ecological studies, yet accurate methods of estimating biological diversity from sampling …

[PDF][PDF] Species richness: estimation and comparison

A Chao, CH Chiu - Wiley StatsRef: statistics reference online, 2016 - researchgate.net
On the basis of the sampling data from an assemblage, estimation of species richness
(observed plus undetected) is statistically difficult especially for highly-diverse assemblages …

Multidimensional biases, gaps and uncertainties in global plant occurrence information

C Meyer, P Weigelt, H Kreft - Ecology letters, 2016 - Wiley Online Library
Plants are a hyperdiverse clade that plays a key role in maintaining ecological and
evolutionary processes as well as human livelihoods. Biases, gaps and uncertainties in …

Coverage‐based rarefaction and extrapolation: standardizing samples by completeness rather than size

A Chao, L Jost - Ecology, 2012 - Wiley Online Library
We propose an integrated sampling, rarefaction, and extrapolation methodology to compare
species richness of a set of communities based on samples of equal completeness (as …