Introduction
Providing accurate biodiversity assessments is a critical goal in
ecology and biogeography with estimations being constantly revised for
some species-rich groups ((1) Costello et al 2017). This issue is
increasingly important given the accelerating human footprint on Earth.
The ongoing worldwide defaunation, characterized by massive population
declines, may trigger the local or even global extinction of rare,
elusive and cryptic species that are still unknown or poorly documented
((2) Barlow et al 2018, (3) Lees & Pimm 2015). Such biodiversity losses
directly impact ecosystem functioning but also human health, well-being
and livelihood ((4) Diaz et al 2018, (5) Duffy et al 2017). This urges
scientists to improve the accuracy and to extend the breadth of
biodiversity inventories and monitoring.
In the marine realm, the detection of species occurrences is
particularly challenging due to the vast volume to monitor, the high
diversity of habitats, the inaccessibility of some areas (e.g. deep sea)
and the behavior of some species (cryptobenthic or elusive) ((6) Juhel
et al 2019, (7) Brandl et al 2018). Environmental DNA (eDNA)
metabarcoding is an emerging tool that can provide more accurate and
wider biodiversity assessments than classical census methods
particularly for rare and elusive species ((8) Garlapati et al 2019, (9)
Boussarie et al 2018, (10) Fukumoto et al 2015). This non-invasive
method is based on retrieving DNA naturally released by organisms in
their environment, amplified by polymerase chain reaction (PCR) and then
sequenced to ultimately identify corresponding species ((11) Ruppert et
al 2019). However, inventorying and monitoring biodiversity using eDNA
metabarcoding requires the completeness of a reference database to
accurately assign each sequence to a given species (e.g. (9) Boussarie
et al. 2018).
By now, only a minority of fish species are present in online DNA
databases for mitochondrial regions targeted by metabarcoding markers,
limiting the extent to which species diversity can be revealed by eDNA.
This proportion of sequenced species is even lower in species-rich
regions and poorly sampled habitats or taxa while the effort to complete
genetic reference databases is long and costly. As an alternative, a
diversity of Operational Taxonomic Units (OTUs) can be extracted from
eDNA metabarcoding through filtering and clustering techniques ((12)
Mahé et al 2014). However, the extent to which the diversity of OTUs
from a limited number of eDNA samples can reveal or predict the
diversity of vertebrate species in a given biodiversity hotspot has not
yet been investigated. This is particularly challenging for
cryptobenthic fish species that are key for reef ecosystems ((13) Brandl
et al 2019) but usually missed by classical surveys ((7) Brandl et al.
2018).
The Bird’s Head Peninsula of West Papua (eastern Indonesia) is located
in the center of the Coral Triangle (marine area extending from Malaysia
to Solomon Islands, (14) Veron et al 2009) which is known to host the
world’s richest marine biodiversity ((15) Allen & Erdmann 2012, (16)
Mangubhai et al 2012). The current checklist of coastal fishes in the
Bird’s Head Peninsula identifies 1,611 species belonging to 508 genera
and 112 families ((17) Kulbicki et al 2013, (15) Allen & Erdmann 2012).
This exceptional level of diversity and endemism is due to a combination
of factors: the complex marine currents and history of sea level changes
((18) Mora et al 2003), vicariance and dispersal at various
spatio-temporal scales ((19) Hubert et al 2017), a variety of habitats
from karsts to many types of coral reefs ((16) Mangubhai et al 2012),
the impact of geographic isolation ((19) Hubert et al 2017), the result
of plates tectonic history ((20) Leprieur et al 2016, (21) Gaboriau et
al 2019) and stable environmental conditions during the quaternary ((22)
Pelissier et al 2014). As a result, Indonesia is endowed with an
exceptional fish diversity which is still poorly known and under severe
threats ((23) Exton et al 2019, (24) Jones et al 2019, (25) Ainsworth et
al 2008). Predicting the level of vertebrate diversity from eDNA OTUs is
thus a critical step in conservation, biogeography and ecology,
particularly in marine biodiversity hotspots.
Here, using eDNA metabarcoding from 92 seawater samples across the
Bird’s Head Peninsula, we (i ) assessed the diversity of coastal
fish species based on an online reference database for the teleo primers
region of the 12S mitochondrial rDNA gene ((26) Valentini et al 2016),
(ii ) estimated the diversity of fish OTUs based on a custom
filtering and clustering bioinformatic pipeline, and (iii ) tested
the capacity of OTU accumulation curves to predict the regional fish
diversity.