Discussion
Our work highlights how abundance-based diversity indices can obscure
changes in community assembly. We quantified this effect by measuring
rarity shifts, and showing how this effect can counteract more familiar
sources of diversity change such as selection (Figure 1). This insight
extends the observation that richness based observations of diversity
change can obscure changes in communities (Chase et al. 2019, Dornelas
et al. 2019); (Urban 2015, Urban et al. 2016). Our results indicate that
strong changes in relative abundances can lead to large shifts in
species’ rarity. These shifts produce the illusion of negligible
diversity change in dynamic communities.
Rarity shifts tended to oppose increases in selection and decreases in
immigration (Figure 4). Increases in diversity from selection and
decreases in diversity from rarity shifts oppose overall diversity
change (Figure 1). This mismatch is commonplace across all studies
(Figure 2). We have shown that rarity shifts are commonplace across many
datasets (Figure 3), particularly in studies where changes in relative
abundances are high studies such as studies experiencing environmental
disturbances (Webb and Scanga 2001, Thorn et al. 2016) or regeneration
(Venturoli et al. 2011). Additionally, studies of annual plant
communities in the Arizonan desert by (Ernest et al. 2009) and
(Lightfoot 2011) experienced strong rarity shifts because measurements
matched or exceeded the seasonal lifespan of the community, meaning
diversity measures reflected the high mortality and rapid emergence of
plant species. Rarity shifts were uncommon in long-term forest plots
where changes in community composition and diversity are slow (Bradford
et al. 2014). Nevertheless, we elect to analyse the data using the
observations, as they were collected, even if, in retrospect, the
sampling periods used may have been comparatively brief. This choice is
likely conservative, as picking longer intervals would likely increase
shifts in relative abundances increasing the importance of rarity
shifts. By analysing the sampling intervals in the original data, our
results illustrate how gradual changes in diversity sometimes imply
rarity shifts and sometimes indicate negligible overall change.
The observations in the previous paragraph highlight the benefits of
focusing on diversity change in plants. Plants are sessile which lowers
the chance that descendants of one species will be confused with
immigrants of the same species. Long-term vegetation plots are available
in many model systems. As a result, data in our study represents 5
continents - North America, South America, Asia and Australia and
Europe. It is of course possible that other sources of change dominate
in other taxa. We suspect for example that immigration will be more
important in other systems.
Our results are one of several recent applications of diversity
partitions. These include analyses of why empirical observations show
seemingly slow shifts in diversity over time (Dornelas et al. 2019), how
to quantify the effects of biotic homogenization (Tatsumi et al. 2020,
Tatsumi et al. 2021, Godsoe et al. 2022), and how to relate biotic
interactions such as competition to shifts in diversity (Godsoe et al.
2021). We have added to this literature by showing that rarity shifts, a
mechanism derived from partitioning (Godsoe et al. 2021), is an
important source of diversity change.
For generations, ecologists have sought to understand the relationship
between changes in diversity, ecosystem functioning, and the fates of
individual species (MacArthur 1965, Blowes et al. 2019). This debate has
become more urgent as we have confronted our limited ability to explain
shifts in diversity in nature (McGill et al. 2015, Socolar et al. 2016,
Urban et al. 2016, Vellend et al. 2017). To help resolve this problem,
we have shown how abundance-based diversity indices can be influenced by
shifts in species rarity. We have provided examples from individual
plots that highlight how these rarity shifts can obscure selection
(Figure 1). We have shown rarity shifts are comparable in magnitude to
selection, and immigration across the 15 studies (Figure 2 and Figure
3). Finally, we have shown rarity shifts can oppose selection and
immigration (Figure 4). Our results highlight how abundance based
diversity measurements can give a disconcertingly slow impression of
diversity change, even in communities with rapid shifts in relative
abundances. Therefore, reliable predictions of diversity change will
require a more nuanced understanding of the role of rarity shifts
Table 1: Summary of the 15 long-term vegetation plots analysed from the
BioTIME database.