Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Malaise Tap Sites
2.2. Processing of Specimens
2.3. Data Analysis
2.4. Extrapolating Species Numbers
- We calculated a Recovery Ratio by dividing the number of BINs detected through sequencing by the species count for each of the 15 families and for all Diptera (BIN/species ratio). This approach generated a ratio for each well-known family, for each DT family, and for all Diptera.
- We estimated the maximum number of species for each “dark taxon” for both Germany and Bavaria by dividing its BIN count by the average BIN/species ratio of all 11 well-known families.
- We estimated the minimum species number for each “dark taxon” by dividing all Diptera BINs by all Diptera species (i.e., 9544). Because this calculation includes numerous families with cryptic diversity, the resultant values underestimate the diversity of the DT families.
3. Results
3.1. Sequencing Results
3.2. Estimation of Taxon Diversity Using BIN/Species Ratios
3.3. Estimation of Taxon Diversity Using Chao1/Species Ratios
3.4. Extrapolating Species Numbers
4. Discussion
4.1. DNA Barcoding: Using BIN Numbers as Proxies for Species Numbers
- Limited geographic sampling as our data originates from few sites in Bavaria only, covering a tiny fraction of habitat types otherwise present.
- Limited funding constrained analysis to just 5% of the 1.2 million specimens that were collected.
4.2. BIN & Chao1/Species Ratios: Well-Known Families versus DT Families
4.3. Discrepancies in Taxa Coverage in Our Malaise Traps
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Site | Trap | Processed Collection Events |
---|---|---|
BFNP 2012 | 1 | 8 May; 22 May; 8 June; 20 June; 4 July; 25 July; 12 August; 3 September; 22 September 2012. |
ZSM-SNSB | 2 | 10 April; 8 May; 5 June; 3 July; 31 July; 28 August; 25 September; 23 October; 20 November; 29 December 2017. |
Allgäu Alps: Oytal | 3 | 4 May; 17 May; 1 June; 16 June; 5 July: 20 July; 7 August; 29 August; 2 October; 27 October 2014. |
Allgäu Alps: Oytal | 4 | 4 May; 17 May; 1 June; 16 June; 5 July: 20 July; 7 August; 29 August; 2 October; 27 October 2014. |
Allgäu Alps: Oytal | 5 | 4 May; 17 May; 1 June; 16 June; 5 July: 20 July; 7 August; 29 August; 2 October; 27 October 2014. |
Allgäu Alps: Oytal | 6 | 4 May; 17 May; 1 June; 16 June; 5 July: 20 July; 7 August; 29 August; 2 October; 27 October 2014. |
Allgäu Alps: Schochen | 7 | 21 June; 4 July; 17 July; 6 August; 4 September; 29 September; 19 October 2014. |
Allgäu Alps: Schochen | 8 | 21 June; 4 July; 17 July; 6 August; 4 September; 29 September; 19 October 2014. |
Allgäu Alps: Schochen | 9 | 21 June; 4 July; 17 July; 6 August; 4 September; 29 September; 19 October 2014. |
Allgäu Alps: Schochen | 10 | 21 June; 4 July; 17 July; 6 August; 4 September; 29 September; 19 October 2014. |
Allgäu Alps: Schochen | 11 | 21 June; 4 July; 17 July; 6 August; 4 September; 29 September; 19 October 2014. |
Allgäu Alps: Koblat | 12 | 23 June, 4 July, 17 July; 8 August; 8 September; 5 September, 27 September; 20 October 2014. |
Allgäu Alps: Koblat | 13 | 23 June, 4 July, 17 July; 8 August; 8 September; 5 September, 27 September; 20 October 2014. |
Allgäu Alps: Koblat | 14 | 23 June, 4 July, 17 July; 8 August; 8 September; 5 September, 27 September; 20 October 2014. |
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Site | Trap | Coordinates | Elevation | Habitat |
---|---|---|---|---|
BFNP | Trap 1 | 48.9509° N 13.422° E | 842 m | Natural forest |
ZSM | Trap 2 | 48.1648° N 11.4849° E | 519 m | Urban, pre-alpine meadow |
Allgäu Alps: Oytal | Trap 3 | 47.39205° N 10.34093° E | 1122 m | Lake rock face |
Allgäu Alps: Oytal | Trap 4 | 47.38903° N 10.34846° E | 1200 m | Cone of scree |
Allgäu Alps: Oytal | Trap 5 | 47.38842° N 10.34440° E | 1056 m | Rough pasture |
Allgäu Alps: Oytal | Trap 6 | 47.38695° N 10.34438° E | 1036 m | River |
Allgäu Alps: Schochen | Trap 7 | 47.39202° N 10.36991° E | 1930 m | Alpine grassland |
Allgäu Alps: Schochen | Trap 8 | 47.39232° N 10.37057° E | 1908 m | Spring |
Allgäu Alps: Schochen | Trap 9 | 47.39368° N 10.36926° E | 2032 m | South-exposed ridge with Blaugras-Horstseggenrasen |
Allgäu Alps: Schochen | Trap 10 | 47.39307° N 10.36229° E | 2010 m | South-exposed rock |
Allgäu Alps: Schochen | Trap 11 | 47.39360° N 10.36615° E | 1980 m | Snow bed |
Allgäu Alps: Koblat | Trap 12 | 47.42223° N 10.34783° E | 2160 m | South-exposed rock face |
Allgäu Alps: Koblat | Trap 13 | 47.42147° N 10.35465° E | 2033 m | Snow bed |
Allgäu Alps: Koblat | Trap 14 | 47.42272° N 10.35730° E | 2005 m | Mountain pine bush |
Taxon | Bavarian Species Count | German Species Count | Species Count Bavaria/Germany |
---|---|---|---|
Asilidae | 68 [28] | 85 [29] | 0.80 |
Calliphoridae | 50 * | 62 [35] | 0.80 * |
Drosophilidae | 64 [28] | 81 [37] | 0.79 |
Ephydridae | 140 * | 174 [38] | 0.80 * |
Muscidae | 267 * | 334 [48] | 0.80 * |
Sarcophagidae | 107 * | 134 [35] | 0.80 * |
Stratiomyidae | 59 [28] | 71 [30,48] | 0.83 |
Syrphidae | 389 [28] | 458 [31] | 0.85 |
Tabanidae | 47 [28] | 58 [8,48] | 0.81 |
Tachinidae | 361 [28] | 501 [48] | 0.72 |
Tipulidae | 120 [33] | 142 [32] | 0.85 |
Cecidomyiidae | 328 [38] | 859 [5,6,7,8] | 0.38 |
Chironomidae | 576 [28] | 781 [5,6,7,8] | 0.74 |
Phoridae | 302 * | 378 [5,6,7,8] | 0.80 * |
Sciaridae | 231 [28] | 343 [43] | 0.67 |
All Diptera | 7635 * | 9544 [8] | 0.80 * |
BFNP | ZSM | Allgäu Alps | Total | |
---|---|---|---|---|
Samples (trap × collection events) | 1 × 9 = 9 | 1 × 10 = 10 | 8 × 7 + 4 × 10 = 96 | 100 |
All | ||||
Specimens | 29,481 | 32,592 | 20,250 | 82,323 |
COI sequences (% success) | 25,217 (85.6%) | 28,923 (88.7%) | 16,152 (79.8%) | 70,293 (85.4%) |
BINs (% new to BOLD) | 2565 (19.4%) | 3870 (15.8%) | 4043 (23.0%) | 8790 (23.8%) |
Diptera | ||||
Specimens (% of all specimens) | 23,114 (78%) | 15,448 (47%) | 14,238 (70%) | 52,800 (64%) |
COI sequences (% success) | 20,909 (91%) | 14,983 (97%) | 12,338 (87%) | 48,230 (91%) |
BINs (in % of all BINs) | 1571 (61%) | 1676 (43%) | 2632 (65%) | 4863 (55%) |
Diptera BINs new to BOLD | 375 | 260 | 736 | 1413 |
DT BINs new to BOLD (% of all new Diptera BINs) | 337 (90%) | 215 (83%) | 215 (29%) | 780 (55%) |
Taxa | BINs | Bavarian Species | German Species | Bavarian/German Species | BINs/Bavarian Species | BINs/German Species |
---|---|---|---|---|---|---|
Asilidae | 13 | 68 | 85 | 0.80 | 0.19 | 0.15 |
Calliphoridae | 22 | 50 | 62 | 0.80 | 0.44 | 0.35 |
Drosophilidae | 27 | 64 | 81 | 0.79 | 0.42 | 0.34 |
Ephydridae | 32 | 140 | 174 | 0.80 | 0.23 | 0.18 |
Muscidae | 160 | 267 | 334 | 0.80 | 0.60 | 0.48 |
Sarcophagidae | 35 | 107 | 134 | 0.80 | 0.33 | 0.26 |
Stratiomyidae | 14 | 59 | 71 | 0.83 | 0.24 | 0.20 |
Syrphidae | 131 | 389 | 458 | 0.85 | 0.34 | 0.29 |
Tabanidae | 9 | 47 | 58 | 0.81 | 0.19 | 0.16 |
Tachinidae | 126 | 361 | 501 | 0.72 | 0.35 | 0.25 |
Tipulidae | 43 | 120 | 142 | 0.85 | 0.36 | 0.30 |
Average values | 0.33 ± 0.9 | 0.27 ± 0.7 | ||||
Cecidomyiidae | 1163 | 328 | 859 | 0.38 | 3.55 | 1.35 |
Chironomidae | 296 | 576 | 781 | 0.74 | 0.51 | 0.38 |
Phoridae | 348 | 302 | 378 | 0.80 | 1.15 | 0.92 |
Sciaridae | 339 | 231 | 343 | 0.72 | 1.47 | 0.99 |
Average values | 1.67 ± 0.9 | 0.91 ± 0.3 | ||||
All Diptera | 4863 | 7635 | 9544 | 0.80 | 0.64 | 0.51 |
Taxon | BINs | Chao1 | BIN/Chao1 | Bavarian Species | German Species | Chao1/ Bavarian Species | Chao1/ German Species |
---|---|---|---|---|---|---|---|
Asilidae | 13 | 16 | 0.81 | 68 | 85 | 0.24 | 0.16 |
Calliphoridae | 22 | 28 | 0.79 | 50 | 62 | 0.56 | 0.45 |
Drosophilidae | 27 | 38 | 0.71 | 64 | 81 | 0.59 | 0.47 |
Ephydridae | 32 | 88 | 0.36 | 140 | 174 | 0.63 | 0.51 |
Muscidae | 160 | 220 | 0.73 | 267 | 334 | 0.82 | 0.66 |
Sarcophagidae | 35 | 41 | 0.85 | 107 | 134 | 0.38 | 0.31 |
Stratiomyidae | 14 | 16 | 0.88 | 59 | 71 | 0.27 | 0.23 |
Syrphidae | 131 | 158 | 0.83 | 389 | 458 | 0.41 | 0.34 |
Tabanidae | 9 | 10 | 0.90 | 47 | 58 | 0.21 | 0.17 |
Tachinidae | 126 | 153 | 0.82 | 361 | 501 | 0.42 | 0.31 |
Tipulidae | 43 | 59 | 0.73 | 120 | 142 | 0.49 | 0.42 |
Average values | 0.46 ± 0.2 | 0.37 ± 0.2 | |||||
Cecidomyiidae | 1163 | 1937 | 0.60 | 328 | 859 | 5.91 | 2.25 |
Chironomidae | 296 | 479 | 0.62 | 576 | 781 | 0.83 | 0.61 |
Phoridae | 348 | 432 | 0.81 | 302 | 378 | 1.43 | 1.14 |
Sciaridae | 339 | 468 | 0.72 | 231 | 343 | 2.03 | 1.36 |
Average values | 2.55 ± 1.7 | 1.34 ± 0.5 | |||||
All Diptera | 4863 | 6927 | 0.70 | 7635 | 9544 | 0.91 | 0.73 |
Dark Taxa | BINs | Estimates Bavaria | Bavarian Species | New Records Bavaria | Estimates Germany | German Species | New Records Germany |
---|---|---|---|---|---|---|---|
BIN/species ratio | |||||||
Cecidomyiidae | 1163 | 1817–3524 | 328 | 1489–3196 | 2280–4307 | 859 | 1421–3448 |
Chironomidae | 296 | 463–897 | 576 | 0–321 | 580–1096 | 781 | 0–315 |
Phoridae | 348 | 544–1055 | 302 | 242–753 | 682–1289 | 378 | 304–911 |
Sciaridae | 339 | 530–1027 | 231 | 299–796 | 665–1256 | 343 | 322–913 |
Chao1/species ratio | |||||||
Cecidomyiidae | 1937 | 2129–4211 | 328 | 1801–3883 | 2653–5235 | 859 | 1794–4376 |
Chironomidae | 479 | 526–1041 | 576 | 0–465 | 656–1295 | 781 | 0–514 |
Phoridae | 432 | 475–939 | 302 | 173–637 | 592–1168 | 378 | 214–790 |
Sciaridae | 468 | 514–1017 | 231 | 283–786 | 641–1265 | 343 | 298–922 |
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Chimeno, C.; Hausmann, A.; Schmidt, S.; Raupach, M.J.; Doczkal, D.; Baranov, V.; Hübner, J.; Höcherl, A.; Albrecht, R.; Jaschhof, M.; et al. Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany. Insects 2022, 13, 82. https://doi.org/10.3390/insects13010082
Chimeno C, Hausmann A, Schmidt S, Raupach MJ, Doczkal D, Baranov V, Hübner J, Höcherl A, Albrecht R, Jaschhof M, et al. Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany. Insects. 2022; 13(1):82. https://doi.org/10.3390/insects13010082
Chicago/Turabian StyleChimeno, Caroline, Axel Hausmann, Stefan Schmidt, Michael J. Raupach, Dieter Doczkal, Viktor Baranov, Jeremy Hübner, Amelie Höcherl, Rosa Albrecht, Mathias Jaschhof, and et al. 2022. "Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany" Insects 13, no. 1: 82. https://doi.org/10.3390/insects13010082
APA StyleChimeno, C., Hausmann, A., Schmidt, S., Raupach, M. J., Doczkal, D., Baranov, V., Hübner, J., Höcherl, A., Albrecht, R., Jaschhof, M., Haszprunar, G., & Hebert, P. D. N. (2022). Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany. Insects, 13(1), 82. https://doi.org/10.3390/insects13010082