High-quality reference genome assemblies have become essential for deepening our understanding of biodiversity, yet obtaining them for many species remains surprisingly challenging. Drawing on experiences from the European Reference Genome Atlas (ERGA) community, we focus on permit and sample-handling procedures leading up to nucleic acid sequencing, covering tasks such as ensuring ethical and legal compliance, verifying accurate species identification, maintaining sample integrity during transport, and isolating high-quality DNA or nuclei. While many of the challenges and solutions we discuss are broadly relevant, our regulatory and logistical examples are primarily from Europe. By synthesising practical guidance, we highlight the crucial importance of taxonomic expertise, proper vouchering and biobanking, rigorous cold-chain management or alternative preservation methods, and emphasise adherence to packaging and shipping requirements for biological materials. We showcase examples spanning diverse regions, taxa and source materials, which underscore the importance of context-specific strategies and internationally harmonised protocols, particularly for metadata reporting. Our recommendations aim to support both small-scale projects and large initiatives, directing collective efforts to facilitate efficient sampling, vouchering and sample processing for future genomic studies.

5 N Karazin Kharkiv National University Kharkiv Ukraine

Berlin Center for Genomics in Biodiversity Research Berlin Germany

Biology Centre of the Czech Academy of Sciences Institute of Entomology Ceske Budejovice Czech Republic

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Vairão Portugal

Biospeleological Society in Bosnia and Herzegovina Sarajevo Bosnia and Herzegovina

Büsgen Institute Department of Forest Genetics and Forest Tree Breeding University of Göttingen Göttingen Germany

Centre for Coastal Research University of Agder Kristiansand Norway

Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway

Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade do Porto Vairão Portugal

Conservation and Evolutionary Genetics Group Estación Biológica de Doñana Seville Spain

Croatian Biospeleological Society Zagreb Croatia

Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal

Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland

Department of Biological Sciences University of New Brunswick Saint John New Brunswick Canada

Department of Biology University of Florence Sesto Fiorentino Italy

Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland

Department of Fish Ecology and Evolution Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland

Department of Systematics Biodiversity and Evolution of Plants University of Göttingen Göttingen Germany

Environmental Bioinformatics Group SIB Swiss Institute of Bioinformatics Lausanne Switzerland

Facultat de Biologia Departament de Genètica Microbiologia i Estadística Universitat de Barcelona Barcelona Spain

Faculty of Biosciences Institute of Cell Biology and Neuroscience Goethe University Frankfurt Frankfurt Germany

Faculty of Environmental Protection Velenje Slovenia

Faculty of Forestry and Wood Sciences Czech University of Life Sciences Prague Czech Republic

Faculty of Mathematics Natural Sciences and Information Technologies University of Primorska Koper Slovenia

Faculty of Pharmacy Department of Pharmacology Pharmacognosy and Botany Complutense University of Madrid Madrid Spain

Faculty of Science Department of Biology University of Sarajevo Sarajevo Bosnia and Herzegovina

Faculty of Science Department of Parasitology BIOCEV Charles University Prague Czech Republic

Finnish Museum of Natural History University of Helsinki Helsinki Finland

Genomics Institute University of California Santa Cruz California USA

Institut de Biologia Evolutiva Biodiversity Program Universitat Pompeu Fabra Barcelona Spain

Institut de Recerca de la Biodiversitat Barcelona Spain

Institute of Biology Dahlem Center of Plant Sciences Freie Universität Berlin Berlin Germany

Institute of Biology Geobotany and Botanical Garden Systematic Botany and Biodiversity Martin Luther University Halle Wittenberg Halle Germany

Institute of Ecology and Evolution Department of Aquatic Ecology and Macroevolution University of Bern Bern Switzerland

Leibniz Institut für Zoo und Wildtierforschung Berlin Germany

LOEWE Centre for Translational Biodiversity Genomics Frankfurt am Main Germany

Museum Koenig Bonn LIB Leibniz Institute for the Analysis of Biodiversity Change Bonn Germany

National Genomics Infrastructure SciLifeLab Uppsala Sweden

Ruder Boskovic Institute Zagreb Croatia

Senckenberg Research Institute Frankfurt Germany

Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden

Uppsala Genome Center Department of Immunology Genetics and Pathology Uppsala University Uppsala Sweden

Zobrazit více v PubMed

10x Genomics Support . 2017. “Salting Out Method for DNA Extraction From Cells (Manual No. CG000116 Rev A; Sample Preparation Demonstrated Protocol).” 1–8. 10× Genomics Inc. https://assets.ctfassets.net/an68im79xiti/375eRsrfeU2YqMsSCc2IMy/476e800d7f3e0dd425b7bb54ad495877/CG000116_SamplePrepDemonstratedProtocol_‐_DesaltingDNAExtractionCells_RevA.pdf.

2009/147/EC . 2009. “Directive on the Conservation of Wild Birds.” https://data.europa.eu/eli/dir/2009/147/2019‐06‐26/eng.

92/43/EEC . 1992. “Council Directive on the Conservation of Natural Habitats and of Wild Fauna and Flora.” https://data.europa.eu/eli/dir/1992/43/2013‐07‐01/eng.

Access to Biological Collections Data Task Group . 2005. “Access to Biological Collection Data (ABCD).” https://www.tdwg.org/standards/115.

Adema, C. M. 2021. “Sticky Problems: Extraction of Nucleic Acids From Molluscs.” Philosophical Transactions of the Royal Society, B: Biological Sciences 376, no. 1825: 20200162. 10.1098/rstb.2020.0162. PubMed DOI PMC

Akimov, I. A. , ed. 2009. Red Data Book of Ukraine. Animals.

Alsos, I. G. , Lavergne S., Merkel M. K. F., et al. 2020. “The Treasure Vault Can Be Opened: Large‐Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material.” Plants 9, no. 4: 432. 10.3390/plants9040432. PubMed DOI PMC

Astrin, J. J. , and Schubert H. C.. 2017. “Community Perception of Natural History Collections—An Online Survey.” Bonn Zoological Bulletin 66, no. 1: 61–72.

Astrin, J. J. , Zhou X., and Misof B.. 2013. “The Importance of Biobanking in Molecular Taxonomy, With Proposed Definitions for Vouchers in a Molecular Context.” ZooKeys 365: 67–70. 10.3897/zookeys.365.5875. PubMed DOI PMC

Aunin, E. , Böhme U., Blake D., et al. 2021. “The Complete Genome Sequence of PubMed DOI PMC

Bakker, F. T. 2019. “Herbarium Genomics: Plant Archival DNA Explored.” In Paleogenomics: Genome‐Scale Analysis of Ancient DNA, 205–224. Springer. 10.1007/13836_2018_40. DOI

Ballare, K. M. , Pope N. S., Castilla A. R., Cusser S., Metz R. P., and Jha S.. 2019. “Utilizing Field Collected Insects for Next Generation Sequencing: Effects of Sampling, Storage, and DNA Extraction Methods.” Ecology and Evolution 9, no. 24: 13690–13705. 10.1002/ece3.5756. PubMed DOI PMC

BBNJ . 2023. “Agreement Under the United Nations Convention on the Law of the Sea on the Conservation and Sustainable Use of Marine Biological Diversity of Areas Beyond National Jurisdiction.” https://www.un.org/bbnjagreement/sites/default/files/2024‐08/Text%20of%20the%20Agreement%20in%20English.pdf.

Beekhof, P. K. , Gorshunska M., and Jansen E. H.. 2012. “Long Term Stability of Paraoxonase‐1 and High‐Density Lipoprotein in Human Serum.” Lipids in Health and Disease 11, no. 1: 53. 10.1186/1476-511X-11-53. PubMed DOI PMC

Bein, B. , Chrysostomakis I., Arantes L. S., et al. 2025. “Long‐Read Sequencing and Genome Assembly of Natural History Collection Samples and Challenging Specimens.” Genome Biology 26, no. 1: 25. 10.1186/s13059-025-03487-9. PubMed DOI PMC

Belaghzal, H. , Dekker J., and Gibcus J. H.. 2017. “Hi‐C 2.0: An Optimized Hi‐C Procedure for High‐Resolution Genome‐Wide Mapping of Chromosome Conformation.” Methods 123: 56–65. 10.1016/j.ymeth.2017.04.004. PubMed DOI PMC

Ben‐Nun, I. F. , Montague S. C., Houck M. L., et al. 2011. “Induced Pluripotent Stem Cells From Highly Endangered Species.” Nature Methods 8, no. 10: 829–831. 10.1038/nmeth.1706. PubMed DOI

Biró, A. , Balázs G., Fišer Ž., Fišer C., Horváth G., and Herczeg G.. 2024. “From Darkness to Twilight: Morphological Divergence Between Cave and Surface‐Subterranean Ecotone PubMed DOI PMC

Blaxter, M. , Archibald J. M., Childers A. K., et al. 2022. “Why Sequence All Eukaryotes?” Proceedings of the National Academy of Sciences of the United States of America 119, no. 4: e2115636118. 10.1073/pnas.2115636118. PubMed DOI PMC

Blaxter, M. , Lewin H. A., DiPalma F., et al. 2025. “The Earth BioGenome Project Phase II: Illuminating the Eukaryotic Tree of Life.” Frontiers in Science 3: 1514835. 10.3389/fsci.2025.1514835. DOI

Blom, M. P. K. 2021. “Opportunities and Challenges for High‐Quality Biodiversity Tissue Archives in the Age of Long‐Read Sequencing.” Molecular Ecology 30, no. 23: 5935–5948. 10.1111/mec.15909. PubMed DOI

Böhne, A. , Fernández R., Leonard J. A., et al. 2024. “Contextualising Samples: Supporting Reference Genomes of European Biodiversity Through Sample and Associated Metadata Collection.” NPJ Biodiversity 3, no. 1: 1–11. 10.1038/s44185-024-00053-7. PubMed DOI PMC

Boisard, J. , Duvernois‐Berthet E., Duval L., et al. 2022. “Marine Gregarine Genomes Reveal the Breadth of Apicomplexan Diversity With a Partially Conserved Glideosome Machinery.” BMC Genomics 23, no. 1: 485. 10.1186/s12864-022-08700-8. PubMed DOI PMC

Borko, Š. , Premate E., Zagmajster M., and Fišer C.. 2023. “Determinants of Range Sizes Pinpoint Vulnerability of Groundwater Species to Climate Change: A Case Study on Subterranean Amphipods From the Dinarides.” Aquatic Conservation: Marine and Freshwater Ecosystems 33, no. 6: 629–636. 10.1002/aqc.3941. DOI

Bryan, T. M. , and Reddel R. R.. 1994. “SV40‐Induced Immortalization of Human Cells.” Critical Reviews in Oncogenesis 5, no. 4: 331–357. 10.1615/critrevoncog.v5.i4.10. PubMed DOI

Buckner, J. C. , Sanders R. C., Faircloth B. C., and Chakrabarty P.. 2021. “The Critical Importance of Vouchers in Genomics.” eLife 10: e68264. 10.7554/eLife.68264. PubMed DOI PMC

Buzan, E. , de Guttry C., Bortoluzzi C., et al. 2024. Harmonising Genomics Research Excellence and Stakeholder Needs in Conservation Management. Authorea. 10.22541/au.172510123.38206942/v1. DOI

Cai, H. , Li Q., Fang X., et al. 2019. “A Draft Genome Assembly of the Solar‐Powered Sea Slug PubMed DOI PMC

Camacho‐Sanchez, M. , Burraco P., Gomez‐Mestre I., and Leonard J. A.. 2013. “Preservation of RNA and DNA From Mammal Samples Under Field Conditions.” Molecular Ecology Resources 13, no. 4: 663–673. 10.1111/1755-0998.12108. PubMed DOI

Campos, P. F. , and Gilbert T. M. P.. 2012. “DNA Extraction From Formalin‐Fixed Material.” In Ancient DNA: Methods and Protocols, edited by Shapiro B. and Hofreiter M., 81–85. Humana Press. 10.1007/978-1-61779-516-9_11. PubMed DOI

Card, D. C. , Shapiro B., Giribet G., Moritz C., and Edwards S. V.. 2021. “Museum Genomics.” Annual Review of Genetics 55: 633–659. 10.1146/annurev-genet-071719-020506. PubMed DOI

Cardoso, A. L. , Oliveira J. I. N., Climaco J. P. S., Venturelli N. B., do Nascimento Moreira C., and Martins C.. 2024. “Conditions for Establishing Fin Primary Cell Cultures in a Wide Range of Ray‐Finned Fishes.” In Vitro Cellular & Developmental Biology. Animal 61: 561–570. 10.1007/s11626-024-00963-7. PubMed DOI

Carroll, S. R. , Garba I., Figueroa‐Rodríguez O. L., et al. 2020. “The CARE Principles for Indigenous Data Governance.” Data Science Journal 19, no. 1: 1–12.

CBD . 2011. “Convention on Biological Diversity.” https://www.cbd.int/convention/text.

Challis, R. , Kumar S., Sotero‐Caio C., Brown M., and Blaxter M.. 2023. “Genomes on a Tree (GoaT): A Versatile, Scalable Search Engine for Genomic and Sequencing Project Metadata Across the Eukaryotic Tree of Life.” Wellcome Open Research 8: 24. 10.12688/wellcomeopenres.18658.1. PubMed DOI PMC

Chorlton, S. D. 2024. “Ten Common Issues With Reference Sequence Databases and How to Mitigate Them.” Frontiers in Bioinformatics 4: 1278228. 10.3389/fbinf.2024.1278228. PubMed DOI PMC

CITES . 1973. “Convention on International Trade in Endangered Species of Wild Fauna and Flora.” https://cites.org/eng/disc/text.php. PubMed

Claw, K. G. , Anderson M. Z., Begay R. L., et al. 2018. “A Framework for Enhancing Ethical Genomic Research With Indigenous Communities.” Nature Communications 9, no. 1: 2957. 10.1038/s41467-018-05188-3. PubMed DOI PMC

Conlon, B. H. , Gostinčar C., Fricke J., et al. 2021. “Genome Reduction and Relaxed Selection Is Associated With the Transition to Symbiosis in the Basidiomycete Genus PubMed DOI PMC

Council of the European Union . 2025. “Russia's War of Aggression Against Ukraine: EU Agrees 17th Package of Sanctions. EU Press Release.” https://www.consilium.europa.eu/en/press/press‐releases/2025/05/20/russia‐s‐war‐of‐aggression‐against‐ukraine‐eu‐agrees‐17th‐package‐of‐sanctions/.

Cubero, O. F. , and Crespo A.. 2002. “Isolation of Nucleic Acids From Lichens.” In Protocols in Lichenology, edited by Kranner I., Beckett R., and Varma A., 381–391. Springer Lab Manuals.

Culver, D. C. , and Pipan T.. 2013. “Subterranean Ecosystems.” In Encyclopedia of Biodiversity, edited by Levin S. A., Second ed., 49–62. Academic Press. 10.1016/B978-0-12-384719-5.00224-0. DOI

Dabney, J. , Knapp M., Glocke I., et al. 2013. “Complete Mitochondrial Genome Sequence of a Middle Pleistocene Cave Bear Reconstructed From Ultrashort DNA Fragments.” Proceedings of the National Academy of Sciences 110, no. 39: 15758–15763. 10.1073/pnas.1314445110. PubMed DOI PMC

Dahn, H. A. , Mountcastle J., Balacco J., et al. 2022. “Benchmarking Ultra‐High Molecular Weight DNA Preservation Methods for Long‐Read and Long‐Range Sequencing.” GigaScience 11: 68. 10.1093/gigascience/giac068. PubMed DOI PMC

Damas, J. , Corbo M., Kim J., et al. 2022. “Evolution of the Ancestral Mammalian Karyotype and Syntenic Regions.” Proceedings of the National Academy of Sciences 119, no. 40: e2209139119. 10.1073/pnas.2209139119. PubMed DOI PMC

Darwin Core Task Group . 2009. “Darwin Core.” http://www.tdwg.org/standards/450.

Davis, C. C. , Sessa E., Paton A., Antonelli A., and Teisher J. K.. 2025. “Guidelines for the Effective and Ethical Sampling of Herbaria.” Nature Ecology & Evolution 9, no. 2: 196–203. 10.1038/s41559-024-02544-z. PubMed DOI

Deakin, J. E. , Potter S., O'Neill R., et al. 2019. “Chromosomics: Bridging the Gap Between Genomes and Chromosomes.” Genes 10, no. 8: 627. 10.3390/genes10080627. PubMed DOI PMC

del Campo, J. , Carlos‐Oliveira M., Čepička I., et al. 2024. “The Protist Cultural Renaissance.” Trends in Microbiology 32, no. 2: 128–131. 10.1016/j.tim.2023.11.010. PubMed DOI

del Campo, J. , Sieracki M. E., Molestina R., Keeling P., Massana R., and Ruiz‐Trillo I.. 2014. “The Others: Our Biased Perspective of Eukaryotic Genomes.” Trends in Ecology & Evolution 29, no. 5: 252–259. 10.1016/j.tree.2014.03.006. PubMed DOI PMC

DeLeo, D. M. , Pérez‐Moreno J. L., Vázquez‐Miranda H., and Bracken‐Grissom H. D.. 2018. “RNA Profile Diversity Across Arthropoda: Guidelines, Methodological Artifacts, and Expected Outcomes.” Biology Methods & Protocols 3, no. 1: bpy012. 10.1093/biomethods/bpy012. PubMed DOI PMC

Delić, T. , Pipan T., Ozimec R., Culver D. C., and Zagmajster M.. 2023. “The Subterranean Species of the Vjetrenica Cave System in Bosnia and Herzegovina.” Diversity 15, no. 8: 912. 10.3390/d15080912. DOI

Delmore, K. E. , and Liedvogel M.. 2020. “Avian Population Genomics Taking Off: Latest Findings and Future Prospects.” In Statistical Population Genomics, edited by Dutheil J. Y., vol. 2090, 413–433. Springer US. 10.1007/978-1-0716-0199-0_17. PubMed DOI

Didukh, Y. P. 2009a. Green Book of Ukraine. Plants. Alterpess. https://greenbook.land.kiev.ua/.

Didukh, Y. P. 2009b. Red Book of Ukraine. Plants. Globalconsulting. https://issuu.com/ecoart/docs/red_book_plants_2009_part1.

DiSSCoTech . 2020. What is a Digital Specimen? DiSSCoTech. https://dissco.tech/2020/03/31/what‐is‐a‐digital‐specimen/.

Driskell, R. R. , and Watt F. M.. 2015. “Understanding Fibroblast Heterogeneity in the Skin.” Trends in Cell Biology 25, no. 2: 92–99. 10.1016/j.tcb.2014.10.001. PubMed DOI

Droege, G. , Barker K., Seberg O., et al. 2016. “The Global Genome Biodiversity Network (GGBN) Data Standard Specification.” Database 2016: baw125. 10.1093/database/baw125. PubMed DOI PMC

Eastman, K. E. , Pendleton A. L., Shaikh M. A., et al. 2023. “A Reference Genome for the Long‐Term Kleptoplast‐Retaining Sea Slug PubMed DOI PMC

EC 338/97 . 1996. “Council Regulation on the Protection of Species of Wild Fauna and Flora by Regulating Trade Therein.” https://eur‐lex.europa.eu/eli/reg/1997/338/oj/eng.

Espinel‐Ingroff, A. , Montero D., and Martin‐Mazuelos E.. 2004. “Long‐Term Preservation of Fungal Isolates in Commercially Prepared Cryogenic Microbank Vials.” Journal of Clinical Microbiology 42, no. 3: 1257–1259. 10.1128/JCM.42.3.1257-1259.2004. PubMed DOI PMC

ETS 104 . 1979. “Convention on the Conservation of European Wildlife and Natural Habitats.” https://rm.coe.int/1680078aff.

Ezaz, T. , O'Meally D., Quinn A. E., Sarre S. D., Georges A., and Marshall Graves J. A.. 2008. “A Simple Non‐Invasive Protocol to Establish Primary Cell Lines From Tail and Toe Explants for Cytogenetic Studies in Australian Dragon Lizards (Squamata: Agamidae).” Cytotechnology 58, no. 3: 135–139. 10.1007/s10616-009-9182-3. PubMed DOI PMC

Federhen, S. 2015. “Type Material in the NCBI Taxonomy Database.” Nucleic Acids Research 43, no. D1: D1086–D1098. 10.1093/nar/gku1127. PubMed DOI PMC

Feigin, C. Y. , Newton A. H., Doronina L., et al. 2018. “Genome of the Tasmanian Tiger Provides Insights Into the Evolution and Demography of an Extinct Marsupial Carnivore.” Nature Ecology & Evolution 2, no. 1: 182–192. 10.1038/s41559-017-0417-y. PubMed DOI

Fekete, Z. , Absolon D. E., Michell C., Wood J. M. D., Goffart S., and Pohjoismäki J. L. O.. 2025. “Chromosome‐Level Reference Genome Assembly for the Mountain Hare ( DOI

Ferreira, M. S. , Thurman T. J., Jones M. R., et al. 2023. “The Evolution of White‐Tailed Jackrabbit Camouflage in Response to Past and Future Seasonal Climates.” Science 379, no. 6638: 1238–1242. 10.1126/science.ade3984. PubMed DOI

Formenti, G. , Theissinger K., Fernandes C., et al. 2022. “The Era of Reference Genomes in Conservation Genomics.” Trends in Ecology & Evolution 37, no. 3: 197–202. 10.1016/j.tree.2021.11.008. PubMed DOI

Frei, D. , Reichlin P., Seehausen O., and Feulner P. G. D.. 2023. “Introgression From Extinct Species Facilitates Adaptation to Its Vacated Niche.” Molecular Ecology 32, no. 4: 841–853. 10.1111/mec.16791. PubMed DOI

Godlevska, L. , Vasyliuk O., Gol'din P., et al. 2018. “Sixth National Report of Ukraine on the Implementation of the Convention on Biological Diversity.”

Gordy, D. , Tashjian R. S., Lee H., Movassaghi M., and Yong W. H.. 2019. “Domestic and International Shipping of Biospecimens.” Methods in Molecular Biology 1897: 433–443. 10.1007/978-1-4939-8935-5_35. PubMed DOI PMC

Gutaker, R. M. , Reiter E., Furtwängler A., Schuenemann V. J., and Burbano H. A.. 2017. “Extraction of Ultrashort DNA Molecules From Herbarium Specimens.” BioTechniques 62, no. 2: 76–79. 10.2144/000114517. PubMed DOI

Hafner, K. , Welt B., Pelletier W., and Boz Özdemir Z.. 2024. “Dry Ice Sublimation Performance as Affected by Binding Agent, Density, and Age.” Engineering Reports 6, no. 9: e12842. 10.1002/eng2.12842. DOI

Hahn, E. E. , Alexander M., Stiller J., Grewe P. M., and Holleley C. E.. 2024. “Hot Alkaline Lysis gDNA Extraction From Formalin‐Fixed Archival Tissues.” PLoS One 19, no. 1: e0296491. 10.1371/journal.pone.0296491. PubMed DOI PMC

Halstead‐Nussloch, G. , Signorini S. G., Giulio M., et al. 2024. “The Genome of the Rayed Mediterranean Limpet PubMed DOI PMC

Hampl, V. , Horner D. S., Dyal P., et al. 2005. “Inference of the Phylogenetic Position of Oxymonads Based on Nine Genes: Support for Metamonada and Excavata.” Molecular Biology and Evolution 22, no. 12: 2508–2518. 10.1093/molbev/msi245. PubMed DOI

He, Z. , Wilson A., Rich F., et al. 2023. “Chromosomal Instability and Its Effect on Cell Lines.” Cancer Reports 6, no. 6: e1822. 10.1002/cnr2.1822. PubMed DOI PMC

Hollingsworth, P. M. 2011. “Refining the DNA Barcode for Land Plants.” Proceedings of the National Academy of Sciences 108, no. 49: 19451–19452. 10.1073/pnas.1116812108. PubMed DOI PMC

Howard, C. , Denton A., Jackson B., et al. 2025. “On the Path to Reference Genomes for All Biodiversity: Lessons Learned and Laboratory Protocols Created in the Sanger Tree of Life Core Laboratory Over the First 2000 Species.” bioRxiv. 10.1101/2025.04.11.648334. PubMed DOI PMC

Hykin, S. M. , Bi K., and McGuire J. A.. 2015. “Fixing Formalin: A Method to Recover Genomic‐Scale DNA Sequence Data From Formalin‐Fixed Museum Specimens Using High‐Throughput Sequencing.” PLoS One 10, no. 10: e0141579. 10.1371/journal.pone.0141579. PubMed DOI PMC

International Committee of the Red Cross . 2024. “How Is the Term “Armed Conflict” Defined in International Humanitarian Law?” International Review of the Red Cross 106, no. 925: 497–522. 10.1017/S1816383124000122. DOI

ITPGRFA . 2009. “International Treaty on Plant Genetic Resources for Food and Agriculture.” https://www.ssrn.com/abstract=4474036.

Kapun, M. , Schwentner M., Haring E., et al. 2025. “Museomics, the Extended Specimen and Collectomics – How to Frame and Name the Diversity of Information Linked to Specimens in Natural History Collections.” Natural History Collections and Museomics 2: 1–21. 10.3897/nhcm.2.161331. DOI

Keane, R. W. , Lindblad P. C., Pierik L. T., and Ingram V. M.. 1979. “Isolation and Transformation of Primary Mesenchymal Cells of the Chick Embryo.” Cell 17, no. 4: 801–811. 10.1016/0092-8674(79)90320-9. PubMed DOI

Keeling, P. J. , and Slamovits C. H.. 2005. “Causes and Effects of Nuclear Genome Reduction.” Current Opinion in Genetics & Development 15, no. 6: 601–608. 10.1016/j.gde.2005.09.003. PubMed DOI

Kenjar, A. , Raj J. R. M., Bhandary J., Girisha B. S., Chakraborty G., and Karunasagar I.. 2021. “Development of a Rapid and Low‐Cost Method for the Extraction of Dermatophyte DNA.” Indian Journal of Dermatology 66, no. 6: 668–673. 10.4103/ijd.ijd_19_21. PubMed DOI PMC

Kistler, L. 2012. “Ancient DNA Extraction From Plants.” In Ancient DNA: Methods and Protocols, edited by Shapiro B. and Hofreiter M., 71–79. Humana Press. 10.1007/978-1-61779-516-9_10. PubMed DOI

Klingström, T. , Bongcam‐Rudloff E., and Pettersson O. V.. 2018. “A Comprehensive Model of DNA Fragmentation for the Preservation of High Molecular Weight DNA.” bioRxiv 2018: 254276. 10.1101/254276. DOI

Kürzel, K. , Kaiser S., Lörz A.‐N., et al. 2022. “Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy.” Frontiers in Marine Science 8: 795196. 10.3389/fmars.2021.795196. DOI

Kuzmina, M. L. , Braukmann T. W. A., Fazekas A. J., et al. 2017. “Using Herbarium‐Derived DNAs to Assemble a Large‐Scale DNA Barcode Library for the Vascular Plants of Canada.” Applications in Plant Sciences 5, no. 12: 1700079. 10.3732/apps.1700079. PubMed DOI PMC

Lalueza‐Fox, C. 2022. “Museomics.” Current Biology 32, no. 21: R1214–R1215. 10.1016/j.cub.2022.09.019. PubMed DOI

Law of Ukraine No. 2818 . 2010. “On the Main Principles (Strategy) of the National Environmental Policy of Ukraine for the Period Until the Year 2020.” https://zakon.rada.gov.ua/go/2818‐17.

Lawniczak, M. K. N. , Davey R. P., Rajan J., et al. 2022. “Specimen and Sample Metadata Standards for Biodiversity Genomics: A Proposal From the Darwin Tree of Life Project.” Wellcome Open Research 7: 187. 10.12688/wellcomeopenres.17605.1. PubMed DOI PMC

Lawniczak, M. K. N. , Kocot K. M., Astrin J. J., et al. 2025. “Best‐Practice Guidance for Earth BioGenome Project Sample Collection and Processing: Progress and Challenges in Biodiverse Reference Genome Creation.” GigaScience 14: giaf041. 10.1093/gigascience/giaf041. PubMed DOI PMC

Lieberman‐Aiden, E. , van Berkum N. L., Williams L., et al. 2009. “Comprehensive Mapping of Long‐Range Interactions Reveals Folding Principles of the Human Genome.” Science 326, no. 5950: 289–293. 10.1126/science.1181369. PubMed DOI PMC

Lukić Bilela, L. , and Jelić D.. 2018. “Caves and Other Subterranean Habitats.” In Chapter 3: Status, Trends and Future Dynamics of Biodiversity and Ecosystems Underpinning Nature's Contributions to People. Chapters of the Regional Assessment Report on Biodiversity and Ecosystem Services for Europe and Central Asia of the IPBES, edited by Brūmelis G. and Troumbis A., 320–326. Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services. https://www.ipbes.net/assessment‐reports/eca.

Lukić, M. , Delić T., Pavlek M., Deharveng L., and Zagmajster M.. 2020. “Distribution Pattern and Radiation of the European Subterranean Genus DOI

Lukić, M. , Jovović L., Bedek J., et al. 2024. “A Practical Guide for the Husbandry of Cave and Surface Invertebrates as the First Step in Establishing New Model Organisms.” PLoS One 19, no. 4: e0300962. 10.1371/journal.pone.0300962. PubMed DOI PMC

Maeda, T. , Takahashi S., Yoshida T., et al. 2021. “Chloroplast Acquisition Without the Gene Transfer in Kleptoplastic Sea Slugs, PubMed DOI PMC

Mangot, J.‐F. , Logares R., Sánchez P., et al. 2017. “Accessing the Genomic Information of Unculturable Oceanic Picoeukaryotes by Combining Multiple Single Cells.” Scientific Reports 7, no. 1: 41498. 10.1038/srep41498. PubMed DOI PMC

Männer, L. , Schell T., Spies J., et al. 2024. “Chromosome‐Level Genome Assembly of the Sacoglossan Sea Slug PubMed DOI PMC

Manzo, E. , Nillies S., Gutiérrez D. G., Panero J. L., Bräuchler C., and Tomasello S.. 2024. “Species Delimitation in DOI

Marinček, P. , Wagner N. D., and Tomasello S.. 2022. “Ancient DNA Extraction Methods for Herbarium Specimens: When Is It Worth the Effort?” Applications in Plant Sciences 10, no. 3: e11477. 10.1002/aps3.11477. PubMed DOI PMC

Marquina, D. , Buczek M., Ronquist F., and Łukasik P.. 2021. “The Effect of Ethanol Concentration on the Morphological and Molecular Preservation of Insects for Biodiversity Studies.” PeerJ 9: e10799. 10.7717/peerj.10799. PubMed DOI PMC

Martin, J. A. , and Wang Z.. 2011. “Next‐Generation Transcriptome Assembly.” Nature Reviews Genetics 12, no. 10: 671–682. 10.1038/nrg3068. PubMed DOI

Mayjonade, B. , Gouzy J., Donnadieu C., et al. 2016. “Extraction of High‐Molecular‐Weight Genomic DNA for Long‐Read Sequencing of Single Molecules.” BioTechniques 61, no. 4: 203–205. 10.2144/000114460. PubMed DOI

Mazzoni, C. J. , Ciofi C., and Waterhouse R. M.. 2023. “Biodiversity: An Atlas of European Reference Genomes.” Nature 619, no. 7969: 252. 10.1038/d41586-023-02229-w. PubMed DOI

McCartney, A. M. , Formenti G., Mouton A., et al. 2024. “The European Reference Genome Atlas: Piloting a Decentralised Approach to Equitable Biodiversity Genomics.” NPJ Biodiversity 3, no. 1: 1–17. 10.1038/s44185-024-00054-6. PubMed DOI PMC

Meiklejohn, K. A. , Damaso N., and Robertson J. M.. 2019. “Assessment of BOLD and GenBank—Their Accuracy and Reliability for the Identification of Biological Materials.” PLoS One 14, no. 6: e0217084. 10.1371/journal.pone.0217084. PubMed DOI PMC

Mérot, C. , Oomen R. A., Tigano A., and Wellenreuther M.. 2020. “A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation.” Trends in Ecology & Evolution 35, no. 7: 561–572. 10.1016/j.tree.2020.03.002. PubMed DOI

Michell, C. T. , Collins J., Laine P. K., et al. 2024. “High Quality Genome Assembly of the Brown Hare ( DOI

Miller, S. A. , Dykes D. D., and Polesky H. F.. 1988. “A Simple Salting Out Procedure for Extracting DNA From Human Nucleated Cells.” Nucleic Acids Research 16, no. 3: 1215. 10.1093/nar/16.3.1215. PubMed DOI PMC

Mills, L. S. , Bragina E. V., Kumar A. V., et al. 2018. “Winter Color Polymorphisms Identify Global Hot Spots for Evolutionary Rescue From Climate Change.” Science 359, no. 6379: 1033–1036. 10.1126/science.aan8097. PubMed DOI

Miranda, I. , Giska I., Farelo L., et al. 2021. “Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel.” Molecular Biology and Evolution 38, no. 10: 4388–4402. 10.1093/molbev/msab177. PubMed DOI PMC

Mollard, R. , and Mahony M.. 2023. “Cell Culture and Karyotypic Description of PubMed DOI PMC

Montoliu‐Nerin, M. , Sánchez‐García M., Bergin C., et al. 2020. “Building De Novo Reference Genome Assemblies of Complex Eukaryotic Microorganisms From Single Nuclei.” Scientific Reports 10, no. 1: 1303. 10.1038/s41598-020-58025-3. PubMed DOI PMC

Nehring, R. 2022. “Digitising Biopiracy? The Global Governance of Plant Genetic Resources in the Age of Digital Sequencing Information.” Third World Quarterly 43, no. 8: 1970–1987. 10.1080/01436597.2022.2079489. PubMed DOI PMC

Niskanen, T. , Lücking R., Dahlberg A., et al. 2023. “Pushing the Frontiers of Biodiversity Research: Unveiling the Global Diversity, Distribution, and Conservation of Fungi.” Annual Review of Environment and Resources 48: 149–176. 10.1146/annurev-environ-112621-090937. DOI

Nurk, S. , Koren S., Rhie A., et al. 2022. “The Complete Sequence of a Human Genome.” Science 376, no. 6588: 44–53. 10.1126/science.abj6987. PubMed DOI PMC

Pawlowski, J. , and Holzmann M.. 2014. “A Plea for DNA Barcoding of Foraminifera.” Journal of Foraminiferal Research 44, no. 1: 62. 10.2113/gsjfr.44.1.62. DOI

Pizarro, D. , Divakar P. K., Grewe F., et al. 2018. “Phylogenomic Analysis of 2556 Single‐Copy Protein‐Coding Genes Resolves Most Evolutionary Relationships for the Major Clades in the Most Diverse Group of Lichen‐Forming Fungi.” Fungal Diversity 92, no. 1: 31–41. 10.1007/s13225-018-0407-7. DOI

Pleijel, F. , Jondelius U., Norlinder E., et al. 2008. “Phylogenies Without Roots? A Plea for the Use of Vouchers in Molecular Phylogenetic Studies.” Molecular Phylogenetics and Evolution 48, no. 1: 369–371. 10.1016/j.ympev.2008.03.024. PubMed DOI

Recknagel, H. , and Trontelj P.. 2022. “From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods.” Bioscience 72, no. 3: 254–266. 10.1093/biosci/biab117. PubMed DOI PMC

Recknagel, H. , Zakšek V., Delić T., Gorički Š., and Trontelj P.. 2024. “Multiple Transitions Between Realms Shape Relict Lineages of PubMed DOI

Redžić, S. , Barudanovic S., and Radević M., eds. 2008. Bosnia and Herzegovina—Land of Diversity. First National Report of Bosnia and Herzegovina for the Convention on Biodiversity. Federal Ministry of Environment and Tourism of Bosnia and Herzegovina.

Rick, J. A. , Brock C. D., Lewanski A. L., Golcher‐Benavides J., and Wagner C. E.. 2024. “Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.” Systematic Biology 73, no. 1: 76–101. 10.1093/sysbio/syad065. PubMed DOI

Ruane, S. , and Austin C. C.. 2017. “Phylogenomics Using Formalin‐Fixed and 100+ Year‐Old Intractable Natural History Specimens.” Molecular Ecology Resources 17, no. 5: 1003–1008. 10.1111/1755-0998.12655. PubMed DOI

Salvador, R. B. , and Cunha C. M.. 2020. “Natural History Collections and the Future Legacy of Ecological Research.” Oecologia 192, no. 3: 641–646. 10.1007/s00442-020-04620-0. PubMed DOI

Sambrook, J. , and Russell D. W.. 2006. “Purification of Nucleic Acids by Extraction With Phenol:Chloroform.” CSH Protocols 2006, no. 1: 4455. 10.1101/pdb.prot4455. PubMed DOI

Saski, M. , Ikechi T., and Makino S.. 1968. “A Feather Pulp Culture Technique for Avian Chromosomes, With Notes on the Chromosomes of the Peafowl and the Ostrich.” Experientia 24, no. 12: 1292–1293. 10.1007/BF02146680. PubMed DOI

Schilthuizen, M. , Vairappan C. S., Slade E. M., Mann D. J., and Miller J. A.. 2015. “Specimens as Primary Data: Museums and ‘Open Science’.” Trends in Ecology & Evolution 30, no. 5: 237–238. 10.1016/j.tree.2015.03.002. PubMed DOI

Schoch, C. L. , Seifert K. A., Huhndorf S., et al. 2012. “Nuclear Ribosomal Internal Transcribed Spacer (ITS) Region as a Universal DNA Barcode Marker for Fungi.” Proceedings of the National Academy of Sciences 109, no. 16: 6241–6246. 10.1073/pnas.1117018109. PubMed DOI PMC

Seluanov, A. , Vaidya A., and Gorbunova V.. 2010. “Establishing Primary Adult Fibroblast Cultures From Rodents.” Journal of Visualized Experiments (JoVE) 44: e2033. 10.3791/2033. PubMed DOI PMC

Shaw, F. , Minotto A., McTaggart S., et al. 2024. “COPO—Managing Sample Metadata for Biodiversity: Considerations From the Darwin Tree of Life Project.” Wellcome Open Research 7: 279. 10.12688/wellcomeopenres.18499.3. PubMed DOI PMC

Shay, J. W. , and Wright W. E.. 2000. “Hayflick, His Limit, and Cellular Ageing.” Nature Reviews Molecular Cell Biology 1, no. 1: 72–76. 10.1038/35036093. PubMed DOI

Sibbald, S. J. , and Archibald J. M.. 2017. “More Protist Genomes Needed.” Nature Ecology & Evolution 1, no. 5. 10.1038/s41559-017-0145. PubMed DOI

Staats, M. , Erkens R. H. J., van de Vossenberg B., et al. 2013. “Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens.” PLoS One 8, no. 7: e69189. 10.1371/journal.pone.0069189. PubMed DOI PMC

Straube, N. , Lyra M. L., Paijmans J. L. A., et al. 2021. “Successful Application of Ancient DNA Extraction and Library Construction Protocols to Museum Wet Collection Specimens.” Molecular Ecology Resources 21, no. 7: 2299–2315. 10.1111/1755-0998.13433. PubMed DOI

Sudmant, P. H. , Kitzman J. O., Antonacci F., et al. 2010. “Diversity of Human Copy Number Variation and Multicopy Genes.” Science 330, no. 6004: 641–646. 10.1126/science.1197005. PubMed DOI PMC

Theissinger, K. , Fernandes C., Formenti G., et al. 2023. “How Genomics Can Help Biodiversity Conservation.” Trends in Genetics 39, no. 7: 545–559. 10.1016/j.tig.2023.01.005. PubMed DOI

Thorburn, D.‐M. J. , Sagonas K., Binzer‐Panchal M., et al. 2023. “Origin Matters: Using a Local Reference Genome Improves Measures in Population Genomics.” Molecular Ecology Resources 23, no. 7: 1706–1723. 10.1111/1755-0998.13838. PubMed DOI

Totoiu, C. A. , Phillips J. M., Reese A. T., et al. 2020. “Vortex Fluidics‐Mediated DNA Rescue From Formalin‐Fixed Museum Specimens.” PLoS One 15, no. 1: e0225807. 10.1371/journal.pone.0225807. PubMed DOI PMC

Trontelj, P. , Blejec A., and Fišer C.. 2012. “Ecomorphological Convergence of Cave Communities.” Evolution 66, no. 12: 3852–3865. 10.1111/j.1558-5646.2012.01734.x. PubMed DOI

Turkalo, T. K. , Maffia A., Schabort J. J., et al. 2023. “A Non‐Genetic Switch Triggers Alternative Telomere Lengthening and Cellular Immortalization in ATRX Deficient Cells.” Nature Communications 14, no. 1: 939. 10.1038/s41467-023-36294-6. PubMed DOI PMC

Twyford, A. D. , Beasley J., Barnes I., et al. 2024. “A DNA Barcoding Framework for Taxonomic Verification in the Darwin Tree of Life Project.” Wellcome Open Research 9: 339. 10.12688/wellcomeopenres.21143.1. PubMed DOI PMC

UNCLOS . 1982. “United Nations Convention on the Law of the Sea.” https://www.un.org/depts/los/convention_agreements/texts/unclos/unclos_e.pdf.

Universal Postal Union & World Customs Organisation . 2024. “WCO–UPU Postal Customs Guide.” https://www.upu.int/UPU/media/upu/files/postalSolutions/programmesAndServices/postalSupplyChain/customs/guideWcoUPUCustomsEn.pdf.

Varma, A. , Padh H., and Shrivastava N.. 2007. “Plant Genomic DNA Isolation: An Art or a Science.” Biotechnology Journal 2, no. 3: 386–392. 10.1002/biot.200600195. PubMed DOI

Vonlanthen, P. , Bittner D., Hudson A. G., et al. 2012. “Eutrophication Causes Speciation Reversal in Whitefish Adaptive Radiations.” Nature 482, no. 7385: 357–362. 10.1038/nature10824. PubMed DOI

Wong, P. B. , Wiley E. O., Johnson W. E., et al. 2012. “Tissue Sampling Methods and Standards for Vertebrate Genomics.” GigaScience 1, no. 1: 2047‐217X‐1‐8. 10.1186/2047-217X-1-8. PubMed DOI PMC

Yamaguchi, K. , Kadota M., Nishimura O., Ohishi Y., Naito Y., and Kuraku S.. 2021. “Technical Considerations in Hi‐C Scaffolding and Evaluation of Chromosome‐Scale Genome Assemblies.” Molecular Ecology 30, no. 23: 5923–5934. 10.1111/mec.16146. PubMed DOI PMC

Zedane, L. , Hong‐Wa C., Murienne J., Jeziorski C., Baldwin B. G., and Besnard G.. 2016. “Museomics Illuminate the History of an Extinct, Paleoendemic Plant Lineage (Hesperelaea, Oleaceae) Known From an 1875 Collection From Guadalupe Island, Mexico.” Biological Journal of the Linnean Society 117, no. 1: 44–57. 10.1111/bij.12509. DOI

Zhao, D. , Salas‐Leiva D. E., Williams S. K., Dunn K. A., and Roger A. J.. 2024. “Eukfinder: A Pipeline to Retrieve Microbial Eukaryote Genomes From Metagenomic Sequencing Data.” bioRxiv 2023: 573569. 10.1101/2023.12.28.573569. PubMed DOI PMC