Introduction
Rapid and cost-effective biodiversity surveillance is a critical,
burgeoning tool in ecology and conservation. DNA metabarcoding, or
high-throughput DNA sequencing of taxonomically informative barcode
genes, has become a well-established tool to efficiently detect many
species from bulk DNA samples for biodiversity surveillance. Such
sequencing is now frequently used to catalog species from the DNA that
organisms shed into the environment (eDNA) (Bohmann et al., 2014). For
example, aquatic vertebrate or invertebrate communities can be detected
with eDNA metabarcoding of water samples (Shaw et al., 2016; Stat et
al., 2017; Valentini et al., 2016), animal diets can be detected from
eDNA metabarcoding of feces (De Barba et al., 2014; Massey et al., in
press; Roffler et al., 2021), and plants and fungi can be detected by
eDNA metabarcoding of pollen or ice core samples (Bell et al., 2019;
Kraaijeveld et al., 2015; Varotto et al., 2021). Similarly, an emerging
technique to monitor the diversity of terrestrial vertebrates uses
animal-feeding invertebrates (whether feeding upon blood, flesh, or
scat) as direct sources of species’ DNA and is called
invertebrate-derived DNA (iDNA) (Batovska et al., 2018;
Calvignac-Spencer et al., 2013; Drinkwater et al., 2019, 2020; Gogarten
et al., 2020; Kocher et al., 2017; P. S. Lee et al., 2016; Schnell et
al., 2012; van der Heyde et al., 2020; D. W. Yu et al., 2012). Similar
to camera traps, a conventional method for terrestrial vertebrate
surveillance, metabarcoding blood, carrion, or fecal meals from iDNA
samplers can be utilized as a non-invasive and efficient method at
profiling a diversity of species in often remote or dense habitats.
However, these methods differ in that camera trapping is strongly biased
for the detection of medium to large terrestrial mammals, with lower
detection probabilities of arboreal species, smaller bodied species, and
other non-mammal taxa (Burton et al., 2015; O’Brien & Kinnaird, 2011).
These drawbacks could make iDNA metabarcoding a more attractive method
for biodiversity monitoring, particularly if iDNA is better able to
detect the birds, amphibians, reptiles, small mammals, and arboreal
mammals that camera trapping often fails to detect.
Leeches (Drinkwater et al., 2019; Schnell et al., 2012, 2018; Weiskopf
et al., 2018) and carrion flies (Calvignac-Spencer et al., 2013; P. S.
Lee et al., 2016; Lynggaard et al., 2019; Rodgers et al., 2017) have
been the primary sources of validating iDNA metabarcoding for monitoring
vertebrate biodiversity. The limited number of studies utilizing
metabarcoding with leeches or carrion flies as iDNA samplers have shown
that both taxa effectively profile biodiversity in remote or difficult
to access environments such as tropical forests (Drinkwater et al.,
2020; Gogarten et al., 2020; P. S. Lee et al., 2016; Weiskopf et al.,
2018). There is a growing literature of comparing carrion flies as iDNA
sources for metabarcoding to camera trapping (Gogarten et al., 2020; P.
S. Lee et al., 2016; Rodgers et al., 2017) but even with their utility
for profiling animal diversity, neither leeches nor carrions flies are
widely collected for other research purposes.
In contrast, some hematophagous insects such as mosquitos and sandflies
are important pathogen vectors worldwide and are routinely sampled for
disease surveillance. Should these pathogen vectors be effective
samplers of vertebrate biodiversity, then using iDNA to profile
biodiversity would be an attractive supplemental and/or complementary
pursuit to other study objectives using vector species (Batovska et al.,
2018; Kocher et al., 2017). We are aware of only one study that has
compared mosquitos and sandflies as iDNA samplers and found that both
were seemingly effective a describing vertebrate diversity (Kocher et
al., 2017). However, these results were not compared to data from a more
established iDNA sampler or to more conventional methods of diversity
surveillance.
A direct comparison of the emerging iDNA samplers (vectors such as
mosquitos and sandflies) to the commonly utilized iDNA taxa groups (such
as carrion flies or leeches) and finally to traditional methods of
biomonitoring (such as camera traps) is needed to evaluate the diversity
revealed by each iDNA source. Such a comparison will set the groundwork
for assessing common biases, benefits, and shortfalls associated with
each method given the current lack of comparison of established methods
to the emerging iDNA samplers of mosquitos and sandflies. Invertebrate
taxa differ in their feeding ecologies and other life history traits,
which can introduce taxonomic biases into biodiversity assessments when
these taxa are used as iDNA sources particularly when utilizing these
methods with small sample sizes or spatial scales. Thus, this comparison
is particularly needed at a spatial scale where these methods can be
evaluated for both alpha and gamma diversity given the same suite of
available species.
Here, we aim to assess the effectiveness of iDNA metabarcoding for
biodiversity surveillance using landscape scale, bulk sampling of insect
groups including carrion flies, sandflies, and mosquitos. We first
compare the three iDNA samplers to camera trapping (the established
method of vertebrate diversity surveillance) to determine if the two
methods reveal similar species richness, composition, and relative
abundance across the sampled landscape. Second, we compare the
biodiversity found with each of the iDNA samplers to assess the
efficiencies and potential biases with using different sources of iDNA
as biomonitoring tools. To achieve these comparisons, we examine both
gamma and alpha diversity with each iDNA sampler and tease apart the
likely causes of dissimilarity.