Published August 12, 2025
| Version v1
Journal article
Open
Navigating uncertainty in museum workflows: genomic data mining and curation of the Diptera collections hosted at RMCA
Authors/Creators
- Esselens, Lore1
- Addison, Pia2
- Bakengesa, Jacqueline3
- Bota, Luis4
- Canhanga, Laura5
- Cugala, Domingos5
- Daniel, Beatriz5
- De Meyer, Marc1
- Delatte, Hélène6
- Herpers, Jean-Marc7
- Jordaens, Kurt1
- Kabota, Sija8
- Kudra, Abdul8
- Majubwa, Ramadhani8
- Manrakhan, Aruna9
- Mussumbe, Mirene5
- Mwatawala, Maulid8
- Theeten, Franck1
- Van den Spiegel, Didier1
- Vanbergen, Sam10
- Vangestel, Carl11
- Virgilio, Massimiliano1
- 1. Royal Museum for Central Africa, Tervuren, Belgium
- 2. University of Stellenbosch, Stellenbosch, South Africa
- 3. Sokoine University of Agriculture, Morogoro, Tanzania|The University of Dodoma, Dodoma, Tanzania
- 4. National Fruit Fly Laboratory, Chimoio, Mozambique|Eduardo Mondlane University, Maputo, Mozambique|Centre of Excellence in Agri-Food Systems and Nutrition, Maputo, Mozambique
- 5. Eduardo Mondlane University, Maputo, Mozambique|Centre of Excellence in Agri-Food Systems and Nutrition, Maputo, Mozambique
- 6. Centre de Coopération Internationale en Recherche Agronomique pour le Développement, La Réunion, France
- 7. Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- 8. Sokoine University of Agriculture, Morogoro, Tanzania
- 9. Citrus Research International, Nelspruit, South Africa
- 10. Royal Museum for Central Africa, Tervuren, Belgium|University of Leuven, Leuven, Belgium
- 11. Royal Belgian Institute of Natural Sciences, Brussels, Belgium|University of Ghent, Ghent, Belgium
Description
As part of its extensive Diptera holdings, the Royal Museum for Central Africa (RMCA) houses over 100,000 specimens of Tephritidae and Syrphidae, which represent a critical resource for taxonomic and systematic research. Here, we present a feasibility study evaluating streamlined workflows for genomic data mining and archiving in museum collections. We analysed DNA yield, quality and sequencing performance from more than 1,400 insect vouchers and found few predictable trends, reflecting the nature of heterogeneous and skewed groups of samples collected under largely unknown field conditions. Regardless, our results show that Illumina short read whole genome sequencing can work well even with degraded insect material. In this context, routine short-read sequencing offers a practical first step for genomic data mining, particularly for large collections. It enables us to reserve more complex and resource-intensive methods for the subset of samples that fail initial sequencing (7% of specimens, in our case). As an outcome of this work, RMCA's archiving system has been adapted to integrate genomic data and metadata alongside traditional specimen records. We argue that genomic data should be treated as an integral component of collection management, enhancing scientific value, supporting long term preservation and improving traceability of genetic resources in natural history collections.
Files
BDJ_article_157274.pdf
Files
(428.4 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:ad2cd30b8d28fc9adec04d7f66c6d7c6
|
428.4 kB | Preview Download |
System files
(155.6 kB)
| Name | Size | Download all |
|---|---|---|
|
md5:4068a0ac5c0ec48e532c2746a8622084
|
155.6 kB | Download |
Linked records
Additional details
References
- Adam M, Theeten F, Herpers J, Vandenberghe T, Semal P, Van den Spiegel D, Duchesne P (2019) DaRWIN: An open source natural history collections data management system. Biodiversity Information Science and Standards 3 https://doi.org/10.3897/biss.3.39054
- Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI (2022) Methodologies for ancient DNA extraction from bones for genomic analysis: approaches and guidelines. Russian Journal of Genetics 58 (9): 1017‑1035. https://doi.org/10.1134/s1022795422090034
- Ballare K, Pope N, Castilla A, Cusser S, Metz R, Jha S (2019) Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods. Ecology and Evolution 9 (24): 13690‑705. https://doi.org/10.1002/ECE3.5756.
- Brecko J, Mathys A, Dekoninck W, Leponce M, VandenSpiegel D, Semal P (2014) Focus stacking: comparing commercial top-end set-ups with a semi-automatic low budget approach. A possible solution for mass digitization of type specimens. ZooKeys 464: 1‑23. https://doi.org/10.3897/zookeys.464.8615
- Brewer GE, Clarkson JJ, Maurin O, Zuntini AR, Barber V, Bellot S, Biggs N (2019) Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms. Frontiers in Plant Science 10 https://doi.org/10.3389/FPLS.2019.01102/BIBTEX
- Brown GW, Starkie ML, Fowler EV, Blacket MJ, Royer JE, Mayer DG, Souza NM, Cheesman J, Missenden B, Irvine M, Schutze MK (2025) Field assessment of current and improved surveillance traps for fruit flies (Diptera: Tephritidae) in Australia. Journal of Economic Entomology https://doi.org/10.1093/jee/toaf085
- Butterwort V, Dansby H, Zink FA, Tembrock LR, Gilligan TM, Godoy A, Braswell WE, Kawahara AY (2022) A DNA extraction method for insects from sticky traps: targeting a low abundance pest, Phthorimaea absoluta (Lepidoptera: Gelechiidae), in mixed species communities. Journal of Economic Entomology 115 (3): 844‑851. https://doi.org/10.1093/jee/toac046
- Card DC, Shapiro B, Giribet G, Moritz C, Edwards SV (2021) Museum genomics. Annual Review of Genetics 55: 633‑659. https://doi.org/10.1146/ANNUREV-GENET-071719-020506/1
- Carter D, Walker A (1999) Care and conservation of natural history collections. Chapter 7: 139‑151.
- Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp:an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34 (17): 884‑890. https://doi.org/10.1093/BIOINFORMATICS/BTY560
- Colella J, Tigano A, MacManes M (2020) A linked-read approach to museomics: higher quality de novo genome assemblies from degraded tissues. Molecular Ecology Resources 20 (4): 856‑70. https://doi.org/10.1111/1755-0998.13155
- Delatte H, Meyer M, Virgilio M (2019) Genetic structure and range expansion of Zeugodacus cucurbitae (Diptera: Tephritidae) in Africa. Bulletin of Entomological Research 109 (6): 713‑22. https://doi.org/10.1017/S0007485319000026
- De Meyer M, Mwatawala M, Copeland R, Virgilio M (2016) Description of new Ceratitis species (Diptera: Tephritidae) from Africa, or how morphological and DNA data are complementary in discovering unknown species and matching sexes. European Journal of Taxonomy 233 https://doi.org/10.5852/ejt.2016.233
- De Meyer M, Goergen G, Jordaens K (2020a) Taxonomic revision of the Afrotropical hover fly genus Senaspis Macquart (Diptera, Syrphidae). ZooKeys 1003: 83‑160. https://doi.org/10.3897/zookeys.1003.56557
- De Meyer M, Goergen G, Jordaens K (2020b) Taxonomic revision of the Afrotropical Phytomia Guérin-Méneville (Diptera: Syrphidae). Zootaxa 4803 (2). https://doi.org/10.11646/zootaxa.4803.2.1
- De Meyer M, Goergen G, Midgley J, Jordaens K (2024) On the identity of the Afrotropical species of Mallota Meigen (Diptera: Syrphidae). European Journal of Taxonomy 958 https://doi.org/10.5852/ejt.2024.958.2675
- Deschepper P, Vanbergen S, Virgilio M, Sciarretta A, Colacci M, Rodovitis V, Jaques J, Bjeliš M, Bourtzis K, Papadopoulos N, De Meyer M (2024a) Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata). Scientific Reports 14 (1). https://doi.org/10.1038/s41598-024-76390-1
- Deschepper P, Vanbergen S, Esselens L, Terblanche J, Karsten M, Snyman M, Cugala D, Canhanga L, Bota L, Mwatawala M, Ramadhani M, Kudra A, Tairo J, Bakengesa J, Addison P, Manrakhan A, Gledel C, Delatte H, De Meyer M, Virgilio M (2024b) A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae). F1000Research 13 https://doi.org/10.12688/f1000research.157946.1
- Ewart K, Johnson R, Ogden R, Joseph L, Frankham G, Lo N (2019) Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species. Molecular Ecology Resources 19 (6): 1578‑1592. https://doi.org/10.1111/1755-0998.13082
- FAO, IAEA (2018) Trapping systems. In: Enkerlin WR, Reyes-Flores J (Eds) Trapping guidelines for area-wide fruit fly programmes. 2nd ed.
- Ferrari G, Esselens L, Hart M, Janssens S, Kidner C, Mascarello M, Peñalba J, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth P (2023) Developing the protocol infrastructure for DNA sequencing natural history collections. Biodiversity Data Journal 11 https://doi.org/10.3897/bdj.11.e102317
- Fowler E, Starkie M, Blacket M, Mayer D, Schutze M (2024) Effect of temperature and humidity on insect DNA integrity evaluated by real-time PCR. Journal of Economic Entomology 117 (5): 1995‑2002. https://doi.org/10.1093/JEE/TOAE193.
- Gauthier J, Pajkovic M, Neuenschwander S, Kaila L, Schmid S, Orlando L, Alvarez N (2020) Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland. Molecular Ecology Resources 20 (5): 1191‑1205. https://doi.org/10.1111/1755-0998.13167
- Gillett CD, Crampton-Platt A, Timmermans MT, Jordal B, Emerson B, Vogler A (2014) Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Molecular Biology and Evolution 31 (8): 2223‑2237. https://doi.org/10.1093/molbev/msu154
- Guschanski K, Krause J, Sawyer S, Valente L, Bailey S, Finstermeier K, Sabin R, Gilissen E, Sonet G, Nagy Z, Lenglet G, Mayer F, Savolainen V (2013) Next-generation museomics disentangles one of the largest primate radiations. Systematic Biology 62 (4): 539‑554. https://doi.org/10.1093/sysbio/syt018
- Hawkins MR, Flores M, McGowen M, Hinckley A (2022) A comparative analysis of extraction protocol performance on degraded mammalian museum specimens. Frontiers in Ecology and Evolution 10 (August). https://doi.org/10.3389/FEVO.2022.984056/BIBTEX
- Kistler L, Ware R, Smith O, Collins M, Allaby R (2017) A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Research 45 (11): 6310‑20. https://doi.org/10.1093/NAR/GKX361
- Knyshov A, Gordon EL, Weirauch C (2019a) Cost‐efficient high throughput capture of museum arthropod specimen DNA using PCR ‐generated baits. Methods in Ecology and Evolution 10 (6): 841‑52. https://doi.org/10.1111/2041-210X.13169.
- Knyshov A, Hoey-Chamberlain R, Weirauch C (2019b) Hybrid enrichment of poorly preserved museum specimens refines homology hypotheses in a group of minute litter bugs (Hemiptera: Dipsocoromorpha: Schizopteridae). Systematic Entomology 44 (4): 985‑95. https://doi.org/10.1111/syen.12368.
- Lee LYC, Wong HY, Lee JY, Waffa ZBM, Aw ZQ, Fauzi SNABM, Hoe SY, Lim ML, Syn CKC (2019) Persistence of DNA in the Singapore Context. International Journal of Legal Medicine 133 (5): 1341‑49. https://doi.org/10.1007/S00414-019-02077-2/METRICS.
- Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (14): 1754‑60. https://doi.org/10.1093/BIOINFORMATICS/BTP324
- Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R (2016) DNA source selection for downstream applications based on DNA quality indicators analysis. Biopreservation and Biobanking 14: 264‑70. https://doi.org/10.1089/bio.2015.0064
- Lund S, Dissing J (2004) Surprising stability of DNA in stains at extreme humidity and temperature. International Congress Series 1261.
- Malakasi P, Bellot S, Dee R, Grace O (2019) Museomics clarifies the classification of Aloidendron (Asphodelaceae), the iconic African tree aloes. Frontiers in Plant Science 10 https://doi.org/10.3389/fpls.2019.01227
- Mandrioli M (2008) Insect collections and DNA analyses: how to manage collections? Museum Management and Curatorship 23 (2): 193‑99. https://doi.org/10.1080/09647770802012375.
- Martoni F, Nogarotto E, Piper A, Mann R, Valenzuela I, Eow L, Rako L, Rodoni B, Blacket M (2021) Propylene glycol and non-destructive DNA extractions enable preservation and isolation of insect and hosted bacterial DNA. Agriculture 11 (1): 77. https://doi.org/10.3390/agriculture11010077
- Mullin V, Stephen W, Arce A, Nash W, Raine C, Notton D, Whiffin A, Blagderov V, Gharbi K, Hogan J, Hunter T, Irish N, Jackson S, Judd S, Watkins C, Haerty W, Ollerton J, Brace S, Gill R, Barnes I (2022) First large‐scale quantification study of DNA preservation in insects from natural history collections using genome‐wide sequencing. Methods in Ecology and Evolution 14 (2): 360‑371. https://doi.org/10.1111/2041-210x.13945
- Nakahama N (2020) Museum specimens: an overlooked and valuable material for conservation genetics. Ecological Research 36 (1): 13‑23. https://doi.org/10.1111/1440-1703.12181
- Orlando L, Allaby R, Skoglund P, Der Sarkissian C, Stockhammer P, Ávila-Arcos M, Fu Q, Krause J, Willerslev E, Stone A, Warinner C (2021) Ancient DNA analysis. Nature reviews methods primers 1 (1). https://doi.org/10.1038/s43586-020-00011-0
- Secretariat Biological Diversity (2011) Nagoya protocol on access to genetic resources and the fair and equitable sharing of benefits arising from their utilization to the convention on biological diversity. United Nations URL: https://www.cbd.int/abs
- Springer Nature (2022) Nature addresses helicopter research and ethics dumping. Nature 606 (7912): 7‑7. https://doi.org/10.1038/d41586-022-01423-6
- Stevens M, Warren G, Mo J, Schlipalius D (2011) Maintaining DNA quality in stored-grain beetles caught in lindgren funnel traps. Journal of Stored Products Research 47 (2): 69‑75. https://doi.org/10.1016/J.JSPR.2010.10.002.
- Straube N, Lyra M, Paijmans JA, Preick M, Basler N, Penner J, Rödel M, Westbury M, Haddad CB, Barlow A, Hofreiter M (2021) Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Molecular Ecology Resources 21 (7): 2299‑2315. https://doi.org/10.1111/1755-0998.13433
- Strijk J, Binh HT, Ngoc NV, Pereira J, Slik JWF, Sukri R, Suyama Y, Tagane S, Wieringa J, Yahara T, Hinsinger D (2020) Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea. PLOS One 15 (5). https://doi.org/10.1371/journal.pone.0232936
- Timmermans MTN, Viberg C, Martin G, Hopkins K, Vogler A (2015) Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections. Biological Journal of the Linnean Society 117 (1): 83‑95. https://doi.org/10.1111/bij.12552
- Zimmermann J, Hajibabaei M, Blackburn D, Hanken J, Cantin E, Posfai J, Evans T (2008) DNA damage in preserved specimens and tissue samples: a molecular sssessment. Frontiers in Zoology 5 (1): 1‑13. https://doi.org/10.1186/1742-9994-5-18/FIGURES/9.
- Zuur AF, Hilbe JM, Ieno EN (2013) A beginner's guide to GLM and GLMM with R: a frequentist and Bayesian perspective for ecologists. Highland Statistics Ltd.