An approach based on the total‐species accumulation curve and higher taxon richness to estimate realistic upper limits in regional species richness

Abstract

Most of accumulation curves tend to underestimate species richness, as they do not consider spatial heterogeneity in species distribution, or are structured to provide lower bound estimates and limited extrapolations. The total‐species (T–S) curve allows extrapolations over large areas while taking into account spatial heterogeneity, making this estimator more prone to attempt upper bound estimates of regional species richness. However, the T–S curve may overestimate species richness due to (1) the mismatch among the spatial units used in the accumulation model and the actual units of variation in β‐diversity across the region, (2) small‐scale patchiness, and/or (3) patterns of rarity of species. We propose a new framework allowing the T–S curve to limit overestimation and give an application to a large dataset of marine mollusks spanning over 11 km2 of subtidal bottom (W Mediterranean). As accumulation patterns are closely related across the taxonomic hierarchy up to family level, improvements of the T–S curve leading to more realistic estimates of family richness, that is, not exceeding the maximum number of known families potentially present in the area, can be considered as conducive to more realistic estimates of species richness. Results on real data showed that improvements of the T–S curve to accounts for true variations in β‐diversity within the sampled areas, small‐scale patchiness, and rarity of families led to the most plausible richness when all aspects were considered in the model. Data on simulated communities indicated that in the presence of high heterogeneity, and when the proportion of rare species was not excessive (>2/3), the procedure led to almost unbiased estimates. Our findings highlighted the central role of variations in β‐diversity within the region when attempting to estimate species richness, providing a general framework exploiting the properties of the T–S curve and known family richness to estimate plausible upper bounds in γ‐diversity.

Incomplete estimates of genetic diversity within species: Implications for DNA barcoding

“…Thus, it becomes difficult to account for correlations that may exist at the subpopulation or higher taxonomic levels. This has been noted in past studies of species richness employing species accumulation and rarefaction curves (Bevilacqua, Ugland, Plicanti, Scuderi, & Terlizzi, 2017;Chiarucci, Bacaro, Ricotta, Palmer, & Scheiner, 2009;Terlizzi, Anderson, Bevilacqua, & Ugland, 2014).…”

A single donor is sufficient to produce a highly functional in vitro antibody library

“…Applying these methods to the single donor library described here, yields a measured HCDR3 diversity of 5.2 × 10 7 at a Hamming 0, which decreases to 2.2 × 10 7 at a Hamming of 3. These values increase to 7.1 × 10 7 (Hamming 0) and 2.7 × 10 7 (Hamming 3) when diversities are estimated using a non-linear regression model 92 . This leads to the conclusion that a significant proportion (>73%) of the true IGHV diversity of natural naive antibody libraries can actually be measured using NovaSeq, regardless of the Hamming distance used.…”

The use of taxonomic relationships among species in applied ecological research: Baseline, steps forward and future challenges

“…For instance, a major issue with estimates of species richness is that, unless the true species richness is known, it is difficult to determine if an estimator is under-or overestimating the actual number of species existing in a given area of interest. The completeness of family-level inventories, in contrast, can be often greater than the completeness of species lists for a given region, and the total number of families can serve as a reference to test the ability of estimators to produce reliable extrapolations (Bevilacqua et al 2018b).…”