Hidden in plain sight

Chimeno, Caroline (2024): Hidden in plain sight: addressing the hidden diversity of German dark taxa using innovative technologies. Dissertation, LMU München: Fakultät für Biologie

Abstract

Studies have shown that in reality, we are drastically underestimating species numbers and that a large proportion of the global diversity is still awaiting discovery or description (Engel et al., 2021; González-Oreja, 2008). Yet the bulk of the planet’s hidden diversity (and biomass) is found in groups that are difficult to study and have therefore received very little taxonomic attention in the past (so-called “dark taxa”) (Hardulak, 2020; Hartop et al., 2022; Hausmann et al., 2020; Meier et al., 2021; Morinière et al., 2019). These groups are so hyperdiverse, that dark taxa have also been referred to as “open-ended” taxa because species number estimates are almost impossible to make (Hartop et al., 2022). The majority of dark taxa are found among two insect orders, Diptera (flies) and Hymenoptera (ants, bees, wasps), and consist in large part of non-brachyceran Diptera such as midges and gnats, as well as parasitoid wasps (Hausmann et al., 2020). Being cryptic diverse, highly abundant, and miniscule (<2 mm), the analysis of these groups is very demanding so often, they are simply cast aside and analysis is limited to better studied and easier-to-handle taxa. At the same time, the fact that dark taxa are so abundant in samples (they can make up more than 70% of specimen numbers) implies that they play an essential in ecological functioning (GBOL III, 2023). Conversely, this means that it is all the more important to make these groups tangible to research so that they can be implemented into conservation measures. If we want to study and describe species more effectively, we need a taxonomic renaissance in descriptive taxonomy (Giangrande, 2003). Morphological methods, which have been used for the last 250 years, alone do not provide sufficient discriminatory information for the tiny, cryptic diverse species of dark taxa. Luckily, recent advances in molecular biology are providing the much-needed means to accelerate species discovery by providing DNA-based discrimination methods (Morinière et al., 2016; Wang et al., 2018). These not only drastically speed-up sample processing and species identifications, these also enable the analysis of entire insect communities in one go (Srivathsan et al., 2015). Also, ever more scientists are recommending the use of integrative workflows which implement methods from different disciplines for species description and delimitation (Meier et al., 2022). Using such complementary approaches increase scientific vigor, as no single method is error-free (Dayrat, 2005; Schlick-Steiner et al., 2010). The main goal of this thesis is to develop an integrative framework for the rapid processing of large samples of dark taxa with three specific objectives. These are (1) identifying the dark diversity in temperate regions, (2) developing an integrative methodology to assess samples of dark taxa, and (3) testing the usability of preservative ethanol of insect bulk samples for metabarcoding applications. The first objective aims at raising awareness for the presence of dark taxa not only in a tropical, but also in a temperate setting (Publications I-III). Data obtained through large-scale DNA barcoding on Malaise trap samples from Padang, Sumatra (2016) and from Germany (2012-2017) were analyzed. The large prevalence of dark taxa in Malaise trap samples (in terms of species diversity and specimen abundance) was demonstrated, and species numbers for four dipteran dark taxa were extrapolated to provide data-based species estimates for Germany. Second, having raised awareness regarding the hidden diversity of dark taxa in temperate regions, a strategy is formulated for tackling one dark taxon from large samples (Publication IV). Using Chironomidae (non-biting midges; Diptera, Nematocera) as a model group, an integrative approach was proposed which includes (i) a three-level subsampling method to reduce the workload of sample processing, (ii) morphology- and (iii) DNA-based methods in parallel to evaluate species diversity, and (iv) examining possible inconsistencies across methods. Here, the results show that with this integrative framework, more than 90% of all species were detected despite having identified only 7% of individuals. Also, the results demonstrate that using either identification method on its own would have been prone to errors that would have gone undetected. Lastly, the usability of ethanol-based DNA for metabarcoding applications is assessed (Publication V). Here, the research question is whether ecological information is conserved in the DNA that is extracted from the collection fluid of bulk samples. If so, this would imply that the usual step of specimen homogenization for DNA extraction can be bypassed because the ethanol of samples can be simply poured out and used for analysis instead. In this manner, all specimens are left intact for further analyzes. Here, the results suggest that ethanol-based DNA does not conserve ecological information and until future research has provided more successful results, it is recommended that researchers dealing with terrestrial ecosystems be careful when using ethanol-based DNA. In conclusion, this thesis builds a framework that combines different disciplines to efficiently study the immense (hidden) insect diversity that is housed in our temperate environments.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: dark taxa, diversity, DNA barcoding, integrative taxonomy, community analysis, metabarcoding
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 19. Februar 2024
• 1. Bericht­erstatter:in: Haszprunar, Gerhard