Prediction of fish species diversity from OTU accumulation
curves
Since the two approaches (taxa and OTUs) underestimated the level of
taxonomic diversity within fish families with a high uncertainty, we
modeled accumulation curves from the diversity of species and OTUs found
across our 92 samples. The modeled asymptote of the assigned species
reached 429 species, a value very close to the 394 sequenced species
present in the Bird’s Head peninsula, but 3.7 times lower than the 1,611
species in the regional checklist (Fig. 4a). Meanwhile, the OTU
accumulation curve reached an asymptote of 1,531, a value very close to
the 1,611 fish species in the Bird’s Head.
Applying this method to the 15 fish families which counted more than 10
OTUs and 10 species in the checklist permitted to assess the ability of
eDNA-based accumulation curves to predict regional fish richness. For
instance, the OTU accumulation curves for the Gobiidae, Labridae and
Pomacentridae, the three richest families (51, 54 and 53 OTUs
respectively), produced asymptotes and thus predictions of fish
diversity much lower than those in the regional checklists with 107.5,
66.1 and 76.2 OTUs, i.e. 47.5%, 81.7% and 69.6% of the checklist
richness respectively (Fig. 4b, c, d).
We then tested the ability of the assigned taxa, the OTUs and the OTU
accumulation curve approaches to predict fish species richness within
families of the regional checklist so the predictive power of linear or
proportional relationships. The total number of assigned taxa per family
in our samples was a significant but weak predictor of the number of
fish species per family in the checklist (R ² = 0.60, p<0.001, Fig. 5a) with the richness of some families being
largely underestimated (e.g. 87.4% of net difference with the checklist
for the Gobiidae, Fig. 5a, d). The number of OTUs per family was a
better predictor of the family species richness in the checklist
(R ² = 0.80, p < 0.001) but left 20% of
unexplained variation among families with still a marked underestimation
(73.3% of net difference with the checklist for Gobiidae, Fig. 5b, e).
Using the asymptotes of OTU accumulation curves, we obtained a high
predictive accuracy of R ² = 0.92 (p < 0.001) for
the species richness within families with less bias for the Gobiidae
(43.7% of net difference with the checklist) (Fig. 5c, f).
In addition, we observed that the net difference between the number of
assigned taxa per family and the number of species per fish family in
the checklist is not related to the number of species of the families
(Fig. 5d) suggesting an absence of systematic bias towards the
underestimation of species-rich families. By contrast, the net
difference between the number of OTUs per fish family and the number of
species per family in the checklist significantly increased
(R 2 = 0.35, p = 0.02) with the number of
species per family (Fig. 5e). This bias towards the underestimation of
species richness within species-rich families is nonetheless avoided
when using the asymptotes of OTU accumulation curves (p = 0.24,
Fig. 5f). Thus, asymptotes of OTU accumulation curves are most accurate
and least biased eDNA-based predictors of fish species diversity within
families in this marine biodiversity hotspot.