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).