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Macroinvertebrate surveys are commonly used for assessing the health of freshwater systems around the world. Traditionally, surveying involves morphologically identifying the families, and sometimes genera, present in samples. Biological indices, derived from taxonomic lists, provide convenient ways to summarise community data and may be fairly ins...
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... were collected from 7 sites in 3 freshwater creeks (Tributary of Devlins, Lalor and Vineyard) in Sydney, Australia (Fig. 1) on multiple occasions between December 2016 and July 2017 (see Supplementary Table S1). On each sampling occasion, three replicate samples were taken from the edges of pools. Edges were sampled with hand-held nets (320 × 250-mm opening; 250-µm mesh) and sweep sampling over transects of approximately 10 m. Macroinvertebrates were ...
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... by the BoBW dataset to detect taxa, varied among genera (Fig. 8) and families (Fig. 9). Increasing the read number threshold reduced the number of taxa that occurred exclusively in the molecular data but also reduced the percentage of genera and families that were shared between the molecular (AIA, BoBW and GenBank) and morphological datasets (Fig. 10). Overall, the morphological dataset shared more taxa with the BoBW dataset than the AIA or GenBank datasets. Whereas the BoBW and AIA datasets had at least some samples with 100% of the families present in the morphological dataset, the GenBank dataset only included 100% of families when a 0% read number threshold was applied and never ...
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... dataset shared more taxa with the BoBW dataset than the AIA or GenBank datasets. Whereas the BoBW and AIA datasets had at least some samples with 100% of the families present in the morphological dataset, the GenBank dataset only included 100% of families when a 0% read number threshold was applied and never included 100% of the genera (Fig. 10). The BoBW dataset was the only dataset to have samples that contained 100% of the genera present in the morphological dataset (Fig. ...
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... some samples with 100% of the families present in the morphological dataset, the GenBank dataset only included 100% of families when a 0% read number threshold was applied and never included 100% of the genera (Fig. 10). The BoBW dataset was the only dataset to have samples that contained 100% of the genera present in the morphological dataset (Fig. ...
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... and prevalence were calculated across all thresholds and are provided as supplementary material (S5 for genera and S6 for families). These calculations were based on the assumption that the morphological identification was correct. For brevity, only those for the BoBW dataset using a read number threshold of 0.1% are provided here for genera (Fig. 11) and families (Fig. 12). Prevalence was highly variable among families and genera, with the majority of taxa having a prevalence below 50%. Prevalence below 10% occurred in 28 of the 59 families and 64 of 101 ...
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... the accuracy of the molecular method was relatively high, with the notable exception of the flatworm Dugesiidae which had a true positive rate of 0% and very high misclassification rate (81.1%) (Fig. 11). However, the primers used in this project are known to not Fig. 5. Pearson's correlation coefficients between morphological taxa richness and richness of molecularly derived OTUs, taxa, and taxa for which SIGNAL grades could be applied. Colour represents datasets and shape of points provide the significance of the correlations. Note ...
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... between precision and true positive rate. The molecular analyses correctly determined the presences/absences for five families and six genera (i.e. F 1 scores = 1): Pionidae Piona (mite), Scirtidae (beetle), Psychodidae Psychoda (true fly), Simuliidae Simulium (true fly), and Culicidae culex (mosquito), and Philopotamidae Chimarra (Caddisfly) (Fig. 11). Generally, most families returned F 1 scores greater than 0.5. However, one or two families within most orders returned null F 1 scores. These were often families that occurred at low prevalence within the samples. However, some occurred at a similar prevalence to other families of their order; for instance, Synthemistidae and ...
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... orders returned null F 1 scores. These were often families that occurred at low prevalence within the samples. However, some occurred at a similar prevalence to other families of their order; for instance, Synthemistidae and Gomphidae both had a prevalence of 0.08, but where the former returned a null F 1 score, the latter returned a score of 0.8 (Fig. ...
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... of the detectability metrics changed with increasing read number threshold (Fig. 13). As read number thresholds are increased, there is a trade-off between decreasing the mean and increasing the spread of values in the true positive rate and increasing the mean and reducing the range of values in the true negative rate. However, all metrics improve with at least some degree of read number filtering while filtering ...
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... by Burgman et al. (2012). An example of this control chart approach is provided by the 25-year long-term study (1995 to 2020) of the Nepean River near the West Camden sewage treatment plant in the Sydney region, Australia, which illustrates the SIGNAL_SG range of morphologically derived scores of about a unit fluctuation as typical variation (see Fig. S1 in Supplementary material). In adopting metabarcoding data as the basis for assessment with biotic indices such as SIGNAL, our study suggests the underlying barcode library will influence slight differences in SIGNAL scores and a period where both morphological and metabarcoding data are obtained would provide an understanding of the ...
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... matched to the misidentified Frontipoda in the molecular analyses. This highlights the issue of incorrectly assigned taxonomy in DNA databases and the need for adequately curated reference libraries, as has been emphasized by other authors (Nilsson et al., 2006;Tixier et al., 2012;Shen et al., 2013;Shackleton and Rees, 2016;Carew et al., 2017). Fig. 10. Boxplots of the percent of genera and families shared between the morphological and molecular datasets and how these percentages change with read number threshold. Fig. 11. Metrics of detectability and prevalence for genera in the BoBW dataset with a read number threshold filter of ...
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... curated reference libraries, as has been emphasized by other authors (Nilsson et al., 2006;Tixier et al., 2012;Shen et al., 2013;Shackleton and Rees, 2016;Carew et al., 2017). Fig. 10. Boxplots of the percent of genera and families shared between the morphological and molecular datasets and how these percentages change with read number threshold. Fig. 11. Metrics of detectability and prevalence for genera in the BoBW dataset with a read number threshold filter of ...
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Citations
... Nevertheless, generating accurate species lists from MBC data is challenging [60]. Thus, the availability of reference sequences linked to known species needs to be developed [17,61]. Several researchers have found that MBC was superior to MOI in single-sample comparisons [62,63]. ...
Background:
The water level of Poyang Lake (China) fluctuates seasonally. Shahu Lake, a smaller body of water connected to Poyang Lake during the wet season, is separated in the dry season. Due to a special fishing method termed 'lake enclosed in autumn', the water level is lowered and reaches its lowest point in January, which is <0.5 m deep in the middle of the lake. Our research investigated the effect of water level changes on the zooplankton community composition in Shahu Lake.
Methods:
We used both DNA metabarcoding method (MBC) (18S rRNA gene V4 region) and morphological method (MOI) to track the zooplankton community structure over four seasons in Shahu Lake (China).
Results:
Totals of 90 and 98 species of zooplankton were detected by MOI and MBC, respectively, with rotifers being the main zooplankton component. The α-diversity index of both methods increased from spring to summer and decreased from summer to autumn, reaching the lowest value in winter. NMDS and a cluster analysis showed that all zooplankton communities detected by MOI and MBC were significantly separated by season. The zooplankton community in winter was separated from that of the other three seasons, but the summer and autumn communities were more similar.
Conclusions:
Changes in the water level had significant effects on the zooplankton community composition. We found that MBC was more able to detect the differences in the zooplankton composition than MOI. MBC also had more advantages in copepod recognition. In our study, 37 species of copepods were detected by MBC, but only 11 species were detected by MOI. We concluded that MBC should be used to research the seasonal variations of zooplankton.
... Sequences with a minimum overlap of 25 bp and homology of at least 80% were merged and only sequences between 301 and 313 bp (i.e. close to the target amplicon length) were retained for further analyses 41 . Sequences were clustered into OTUs, using a 97% clustering threshold as this threshold corresponds reasonably well with COI delimitation between invertebrate species 42 . ...
... gov/ genba nk/, accessed 10th of June 2021). We then refined this taxonomic assignment using percent homology thresholds, arbitrarily assigned as part of the GHAP pipeline: 97% or greater for species, 95 to < 97% for genus, 90 to < 95% for family, 85-< 90% for order, and those with < 85% were not assigned because of taxonomic uncertainty 41 . ...
Platypuses ( Ornithorhynchus anatinus ) forage for macroinvertebrate prey exclusively in freshwater habitats. Because food material in their faeces is well digested and mostly unidentifiable, previous dietary studies have relied on cheek pouch assessments and stable isotope analysis. Given DNA metabarcoding can identify species composition from only fragments of genetic material, we investigated its effectiveness in analysing the diet of platypuses, and to assess variation across seasons and sexes. Of the 18 orders and 60 families identified, Ephemeroptera and Diptera were the most prevalent orders, detected in 100% of samples, followed by Trichoptera, Pulmonata, and Odonata (86.21% of samples). Caenidae and Chironomidae were the most common families. Diptera had a high average DNA read, suggesting it is an important dietary component that may have been underestimated in previous studies. We found no variation in diet between sexes and only minimal changes between seasons. DNA metabarcoding proved to be a highly useful tool for assessing platypus diet, improving prey identification compared to cheek pouch analysis, which can underestimate soft-bodied organisms, and stable isotope analysis which cannot distinguish all taxa isotopically. This will be a useful tool for investigating how platypus prey diversity is impacted by habitat degradation as a result of anthropogenic stressors.
... Astonishingly, these rapid advances in eDNA-based technologies are rather timidly implemented in routine biomonitoring (Hering et al., 2018;Shackleton et al., 2021). Although the concept of Biomonitoring 2.0 is widely endorsed, its acceptance in practice is hampered for various reasons. ...
... Astonishingly, these rapid advances in eDNA-based technologies are rather timidly implemented in routine biomonitoring (Hering et al., 2018;Shackleton et al., 2021). Although the concept of Biomonitoring 2.0 is widely endorsed, its acceptance in practice is hampered for various reasons. ...
