1 Introduction
In the past decades, natural environments have been disturbed and
destroyed worldwide at alarming rates, which results in a large loss of
species (Barnosky et al., 2011; Stork, 2018). In hyperdiverse
ecosystems, such as those in the Neotropical region, several species
could go extinct before even being identified (Bradshaw et al., 2011;
Laurance, 1999). This indicates that biodiversity evaluation needs to be
accelerated by combining the strengths of molecular biology, sequencing
technology, and bioinformatics to recognize previously known and
described species (Gostel & Kress, 2022), and to allow new findings. In
this context, DNA-based approaches have become increasingly useful and
promising tools for estimating diversity and guaranteeing rapid and
accurate identification of species. Since the proposal of the DNA
barcoding technique, using a short standard genetic marker for
species-level identification and cryptic species detection (Hebert et
al., 2003; Hebert et al., 2004), the procedure has been becoming
progressively popular among conservationists and taxonomists (Farooq et
al., 2020; Pearlet al., 2022), and paved the way for biological
monitoring using metabarcoding (e.g., Steinke et al., 2022).
Aquatic insects play a crucial role for the equilibrium of aquatic
ecosystems because of their complex life cycle, which distinguishes them
from exclusively aquatic or terrestrial life forms, and generates a
differentiated potential for understanding biogeographical and
ecological research. It is therefore paramount to invest in knowledge of
the diversity of these organisms, as they are extremely rich both in
functionality and species numbers. Non-biting midges (Diptera:
Chironomidae) are true flies, and frequently dominate aquatic insect
communities in both abundance and species richness. It is a cosmopolitan
group, occurring in an enormous variety of aquatic ecosystems, in all
biogeographical regions of the world, including Antarctica. Presumably,
the great species and habitat diversity in this family is a product of
its antiquity, relatively low vagility and evolutionary plasticity
(Ferrington, 2008), which makes the family not only a valuable source of
indicator species for lentic and lotic aquatic ecosystems, but also one
of the most interesting groups for phylogenetic and biogeographical
analyses (Silva & Ekrem, 2016).
The advantage of dealing with hyperdiverse taxa is that they surely
exhibit several repeated patterns, which may provide evidence of
underlying processes (Coscaron et al., 2009). Therefore, a genus such asPolypedilum , widespread and rich in species, may be suitable for
biogeographical and ecological research, as the diversity of these
insects is strongly linked with the conservation of aquatic habitats.Polypedilum is one of the largest chironomid genera containing
about 440 described species (Sæther et al., 2010). Larvae ofPolypedilum occur in nearly all types of still and flowing
waters. Knowledge of their community compositions is essential due to
their potential as bioindicators, since natural or man-made shifts have
impact on them, and consequently in ecosystem processes. However, whilst
most studies rather focus on taxonomic or phylogenetic issues (e.g.,
Bidawid & Fittkau, 1995; Bidawid-Kafka, 1996; Sæther & Sundal, 1999;
Vårdal et al., 2002; Sæther & Oyewo, 2008; Oyewo & Sæther, 2008;
Shimabakuro, et al., 2019; Pinho & Silva, 2020), so far there have been
only few detailed studies on the species richness and species turnover
of the hyperdiverse Chironomidae (Lin et al., 2015; Song et al., 2018).
The biota of South America always has attracted the attention of
naturalists because of the interesting distributional patterns exhibited
by its flora and fauna (Hooker, 1844-47; Darwin, 1859; Wallace, 1876).
For more than a century, biogeographers have proposed theories to
explain the origin and relationships of the biodiversity found in South
America and other southern temperate regions such as Australia, New
Zealand and South Africa (Silva & Farrell, 2017). Moreover, the region
is a preferred target for investigating the function of these components
in the dynamic of diversification, both by harboring the majority of the
Earth’s species and extending across temperate and tropical belts. The
high number of species in South America, on a regional as well as on a
continental scale, makes the region an important reference mark for
estimation of biodiversity loss. However, for the Neotropical non-biting
midge fauna, the knowledge of the actual species diversity is
fragmentary and formal identifications often are unachievable (Spies &
Reiss, 1996).
Usually, automated species delimitation approaches are considered
particularly useful in organisms with uncertain species boundaries, due
to fragmentary taxonomic knowledge or signals in phylogenetic inferences
being obscured by lineage sorting or introgression (O’Meara, 2010 and
references therein). In this sense, several methods for species
delimitation have been developed and applied, for instance, the
Automatic Barcode Gap Discovery – ABGD (Puillandre et al., 2012), the
Barcode Index Number – BIN (Ratnasingham & Hebert, 2013), the
Generalized Mixed Yule Coalescent – GMYC (Pons et al., 2006), the
Poisson Tree Processes – PTP (Zhang et al., 2013). Despite these
approaches being suitable to delimit species, they can occasionally lead
to uncertainty in genetic diversity estimates due to either
oversplitting or overlumping of the taxa. Therefore, the integration of
different algorithms is needed for accurate species delimitation. In
this study, we first compare the performance of different methods of
species estimation and evaluate how much these different approaches
affect estimates of putative species richness in South America. We then
test the hypothesis that there will be substantial differences in
community structure between the Polypedilum fauna in South
America, considered more diverse, and neighboring regions, particularly
the Nearctic.