A conceptual guide to measuring species diversity

Abstract

Three metrics of species diversity – species richness, the Shannon index and the Simpson index – are still widely used in ecology, despite decades of valid critiques leveled against them. Developing a robust diversity metric has been challenging because, unlike many variables ecologists measure, the diversity of a community often cannot be estimated in an unbiased way based on a random sample from that community. Over the past decade, ecologists have begun to incorporate two important tools for estimating diversity: coverage and Hill diversity. Coverage is a method for equalizing samples that is, on theoretical grounds, preferable to other commonly used methods such as equal‐effort sampling, or rarefying datasets to equal sample size. Hill diversity comprises a spectrum of diversity metrics and is based on three key insights. First, species richness and variants of the Shannon and Simpson indices are all special cases of one general equation. Second, richness, Shannon and Simpson can be expressed on the same scale and in units of species. Third, there is no way to eliminate the effect of relative abundance from estimates of any of these diversity metrics, including species richness. Rather, a researcher must choose the relative sensitivity of the metric towards rare and common species, a concept which we describe as ‘leverage.' In this paper we explain coverage and Hill diversity, provide guidelines for how to use them together to measure species diversity, and demonstrate their use with examples from our own data. We show why researchers will obtain more robust results when they estimate the Hill diversity of equal‐coverage samples, rather than using other methods such as equal‐effort sampling or traditional sample rarefaction.

Biogeography, diversity and environmental relationships of shelf and deep-sea benthic Amphipoda around Iceland

“…4A ), its sole use is usually not encouraged as it is heavily affected by sample size and shows high sensitivity in recording rare species ( Jost, 2006 ). There were some profound differences between Hill numbers—species richness, Shannon, and Simpson diversity—likely because each of these indices scales rarity differently ( Chao, Chiu & Jost, 2014 ; Roswell, Dushoff & Winfree, 2021 ; Figs. 4B , 4C ).…”

“…The Simpson index, on the other hand, is considered as being most robust when sampling effort differs strongly between samples, since it largely reflects patterns in the most common species ( Jost, 2006 ). Shannon diversity can be seen as a intermediate measure in terms of its responses to sample size and rarity ( Roswell, Dushoff & Winfree, 2021 ). Overall, though, all estimates applied have their merits and pitfalls, and typically using all three indices provides the best representation of the diversity in a given area ( Roswell, Dushoff & Winfree, 2021 ).…”

“…Shannon diversity can be seen as a intermediate measure in terms of its responses to sample size and rarity ( Roswell, Dushoff & Winfree, 2021 ). Overall, though, all estimates applied have their merits and pitfalls, and typically using all three indices provides the best representation of the diversity in a given area ( Roswell, Dushoff & Winfree, 2021 ). Nevertheless, a consistent pattern of a higher diversity in the shallows—relative to the deep clusters—was evident in all three indices.…”

Differential responses of amphibians and reptiles to land-use change in the biodiversity hotspot of north-eastern Madagascar

“…To compare the evenness of communities between land-use types, we additionally plotted the observed and extrapolated diversity across hill numbers for each land-use type, allowing for a direct comparison of slopes between land-use types (Chao and Jost 2015; Roswell et al 2021).…”

“…the effective number of species in the community, giving equal weight to frequent and infrequent species; q=1 (1D) as Shannon diversity, giving more weight to more frequently observed species and q=2 (2D), as Simpson diversity interpreted as the effective number of abundant species. This approach is now well established given key advantages over traditional Shannon and Simpson diversity indices (Roswell et al 2021).…”