Abstract

Long-term ecological studies have consistently reported slower than expected changes in biodiversity over time. One explanation for this phenomenon is that commonly used diversity measurements such as species richness are too coarse to detect mechanisms shaping community assembly. It remains unclear whether abundance based diversity measurements are susceptible to the same problem. To test this, we study temporal changes in abundance based diversity indices across 3341 observations from 880 plots from 15 long-term vegetation plot studies. We then partition diversity change into mechanisms of interest to ecologists: selection, drift, and immigration. We show that these mechanisms are an imperfect predictor of temporal diversity change, creating a mismatch between changes in species abundances and changes in diversity, particularly when shifts in diversity are rapid. To resolve this mismatch, we quantify a less studied mechanism “rarity shifts”, which measure how an individual’s contributions to diversity changes over time. We found rarity shifts are an important component of diversity change across many studies. Furthermore, rarity shifts tend to oppose other mechanisms, particularly selection. Therefore, rarity shifts obscure changes in relative abundance from abundance based diversity measurements, revealing why diversity changes appear slower than expected. Ultimately, understanding rarity shifts can lead to a more accurate understanding of the rate and nature of temporal diversity change in ecology and conservation.
Key Words: Biodiversity, species richness, mechanistic models, partition, selection, immigration, Shannon entropy, Gini-Simpsons
Introduction
A central goal of ecology is to understand biodiversity change over time (MacArthur 1965, McGill et al. 2015, Dornelas et al. 2018, Chase et al. 2019, Dornelas et al. 2019). Biodiversity represents the variety of living organisms found in a given place. Biodiversity is a key concept in conservation, used to assess ecosystem health in response to management or anthropogenic stressors and to prioritize areas for protection (McGill et al. 2015, Hillebrand et al. 2018). Despite disruptive anthropogenic environmental changes, many long-term ecological studies show surprisingly little change in biodiversity within locations (Sax et al. 2002, Vellend et al. 2013, Vellend et al. 2017, Hillebrand et al. 2018). For example, analyses of vegetation plots show no overall decline in local scale biodiversity over time (Vellend et al. 2013). Surprisingly, this apparent stasis concealed important trends in community assembly: the rate of extinctions increased over time, but this effect was obscured by an increase in the rate of colonisations (Dornelas et al. 2019). Given the need to predict shifts in biodiversity (Urban et al. 2016), there is a need to understand the extent of this mismatch.
Species richness, the most widely studied diversity measurement, may give an overly coarse picture of diversity change (Hillebrand et al. 2018). This is because richness provides no explicit information about species abundances, and many of the mechanisms that operate in communities act on abundances (MacArthur 1965, Urban et al. 2016, Godsoe et al. 2023). The logical alternative is abundance-based diversity indices such as Shannon entropy and Gini-Simpson’s (Jost 2006). These metrics incorporate information on the evenness of species’ relative abundances in addition to richness.
When studying changes in abundance based diversity indices, it makes sense to focus on mechanisms that change relative abundances such as selection and drift at the species level (Vellend 2016). A major advantage of this approach is that selection describes changes in relative abundances and diversity summarizes information on relative abundances (Jost 2006). In contrast, species interactions such as competition or predation are characterized by their effects on absolute abundances. Competition, for example, decreases the absolute abundance of some species at the expense of others, while predation increases the absolute abundance of predators and decreases the absolute abundance of prey (Holland and DeAngelis 2009). By focusing on selection and drift, we are implicitly capturing some of the consequences of species interactions (Vellend 2010), but multiple species interactions can have indistinguishable effects on diversity (Godsoe et al. 2023).
To quantify the effects of mechanisms that alter diversity, Godsoe et al. (2021) proposed partitioning diversity change for abundance-based diversity measurements. This approach starts by measuring each individual’s contribution to a diversity index, with individuals belonging to rare species contributing more than individuals belonging to common species (Patil and Taillie 1982, Roswell et al. 2021). Overall diversity change is then decomposed into changes in individual contributions. For example, species-level selection occurs when individuals belonging to rare species have higher fitness than individuals belonging to common species. Species-level drift occurs when chance events lead to differences in the number of descendants produced by individuals belonging to rare species relative to common species. Note that, in small, observational studies drift and selection can produce similar effects (i.e. a change in the relative abundances of individuals from species that were already in the community). For this reason, we describe drift under the term “selection”, but see Godsoe et al. (2022), for a simulation-based test for the effects of drift in larger plots.
Under some circumstances, partitioning emphasizes the role of mechanisms familiar to ecologists. For example, Figure 1 illustrates changes in relative abundances in observations of forest plots in Brazil (Farah et al. 2014) from the BioTIME database (Dornelas et al. 2018). In this case, the relative abundance of a rare species Psychotria vauthieri slightly increased, while the relative abundance of a common species Ixora gardneriana (Figure 1A) slightly decreased between 1994 and 1999. This leads to a small increase in diversity (Figure 1C). There was no immigration in this community, and the total change in diversity is more or less equal to the increase in selection from rare species becoming more common in the plot (Figure 1E). In contrast, rapid changes in relative abundances can lead to a mismatch between total change in diversity and mechanisms changing relative abundances. For example, the right column in Figure 1 illustrates forest plots with far more dramatic changes in relative abundances. In 1994 Plinia cauliflora is the rarer species while Croton floribundus is more common. However, P. cauliflora increases in relative abundance to become more common than C. floribundus in 1999. This dramatic flip in relative abundances produces a small change in diversity (Figure 1 D) which is similar to the diversity change recorded in the first forest plot (Figure 1C). This is because the success of rare species, which is captured by the selection term, increasing diversity, is counteracted by the rapid changes in rarity exhibited. The opposing mechanisms of rarity shifts and selection in this example explained why diversity changes were smaller in magnitude than expected; highlighting how a mismatch between relative abundances and diversity change may arise (Figure 1 F).