Pyke, G. H. & Ehrlich, P. R. Biological collections and ecological/environmental research: A review, some observations and a look to the future. Biol. Rev. 85, 247266 (2010).

Article PubMed Google Scholar

Wheeler, Q. D. et al. Mapping the biosphere: Exploring species to understand the origin, organization and sustainability of biodiversity. Syst. Biodivers. 10, 120 (2012).

Article CAS Google Scholar

Lane, M. A. Roles of natural history collections. Ann. Mo. Bot. Gard. 83, 536545 (1996).

Article Google Scholar

Raxworthy, C. J. & Smith, B. T. Mining museums for historical DNA: Advances and challenges in museomics. Trends Ecol. Evol. 36, 10491060 (2021).

Article CAS PubMed Google Scholar

Cavill, E. L., Liu, S., Zhou, X. & Gilbert, M. T. P. To bee, or not to bee? One leg is the question. Mol. Ecol. Resour. 22, 18681874 (2022).

Article CAS PubMed Google Scholar

OBrien, D. et al. Bringing together approaches to reporting on within species genetic diversity. J. Appl. Ecol. 59, 22272233 (2022).

Article Google Scholar

Pearman, P. B. et al. Monitoring of species genetic diversity in Europe varies greatly and overlooks potential climate change impacts. Nat. Ecol. Evol. 2024, 115. https://doi.org/10.1038/s41559-023-02260-0 (2024).

Article Google Scholar

Gauthier, J. et al. Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland. Mol. Ecol. Resour. 20, 11911205 (2020).

Article CAS PubMed PubMed Central Google Scholar

Jensen, E. L. et al. Ancient and historical DNA in conservation policy. Trends Ecol. Evol. 37, 420429 (2022).

Article CAS PubMed Google Scholar

Fountain, T. et al. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly. Proc. Natl. Acad. Sci. USA 113, 26782683 (2016).

Article ADS CAS PubMed PubMed Central Google Scholar

Dabney, J., Meyer, M. & Pbo, S. Ancient DNA damage. Cold Spring Harb. Perspect. Biol. 5, 012567 (2013).

Article Google Scholar

Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 1461614621 (2007).

Article ADS CAS PubMed PubMed Central Google Scholar

Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3e3 (2012).

Article CAS PubMed Google Scholar

Campos, P. F. & Gilbert, M. T. P. DNA extraction from keratin and chitin. Methods Mol. Biol. 1963, 5763 (2019).

Article CAS PubMed Google Scholar

Chen, F., Shi, J., Luo, Y. Q., Sun, S. Y. & Pu, M. Genetic characterization of the gypsy moth from China (Lepidoptera, Lymantriidae) using inter simple sequence repeats markers. PLoS ONE 8, e73017 (2013).

Article ADS CAS PubMed PubMed Central Google Scholar

Palma, J., Valmorbida, I., da Costa, I. F. D. & Guedes, J. V. C. Comparative analysis of protocols for DNA extraction from soybean caterpillars. Genet. Mol. Res. 15, 15027094 (2016).

Article Google Scholar

Blaimer, B. B., Lloyd, M. W., Guillory, W. X. & Brady, S. G. Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens. PLoS ONE 11, e0161531 (2016).

Article PubMed PubMed Central Google Scholar

Marn, D. V., Castillo, D. K., Lpez-Lavalle, L. A. B., Chalarca, J. R. & Prez, C. R. An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae). MethodsX 8, 101255 (2021).

Article PubMed PubMed Central Google Scholar

Thomsen, P. F. et al. Non-destructive sampling of ancient insect DNA. PLoS ONE 4, e5048 (2009).

Article ADS PubMed PubMed Central Google Scholar

Lalonde, M. M. L. & Marcus, J. M. How old can we go? Evaluating the age limit for effective DNA recovery from historical insect specimens. Syst. Entomol. 45, 505515 (2020).

Article Google Scholar

Latorre, S. M. et al. Museum phylogenomics of extinct Oryctes beetles from the Mascarene Islands. bioRxiv https://doi.org/10.1101/2020.02.19.954339 (2020).

Article Google Scholar

Cavill, E. & Liu, S. To bee, or not to bee? One leg is the question. Mol. Ecol. Resour. 22, 18681874 (2022).

Article CAS PubMed Google Scholar

Starks, P. T. & Peters, J. M. Semi-nondestructive genetic sampling from live eusocial wasps, Polistes dominulu and Polistes fuscatu. Insectes Soc. 49, 2022 (2002).

Article Google Scholar

Gilbert, M. T. P., Moore, W., Melchior, L. & Worobey, M. DNA extraction from dry museum beetles without conferring external morphological damage. PLoS ONE 2, e272 (2007).

Article ADS PubMed PubMed Central Google Scholar

Korlevi, P. et al. A minimally morphologically destructive approach for DNA retrieval and whole-genome shotgun sequencing of pinned historic dipteran vector species. Genome Biol. Evol. 13, 226 (2021).

Article Google Scholar

Kristensent, N. P., Scoble, M. J. & Karsholt, O. Lepidoptera phylogeny and systematics: The state of inventorying moth and butterfly diversity. Zootaxa 1668, 699747 (2007).

Google Scholar

Neff, F. et al. Different roles of concurring climate and regional land-use changes in past 40 years insect trends. Nat. Commun. 13, 7611 (2022).

Article ADS CAS PubMed PubMed Central Google Scholar

Wagner, D. L., Grames, E. M., Forister, M. L., Berenbaum, M. R. & Stopak, D. Insect decline in the Anthropocene: Death by a thousand cuts. Proc. Natl. Acad. Sci. USA 118, 39891188 (2021).

Article Google Scholar

Casas-Marce, M., Revilla, E. & Godoy, J. A. Searching for DNA in museum specimens: A comparison of sources in a mammal species. Mol. Ecol. Resour. 10, 502507 (2010).

Article CAS PubMed Google Scholar

Silva, P. C., Malabarba, M. C., Vari, R. & Malabarba, L. R. Comparison and optimization for DNA extraction of archived fish specimens. MethodsX 6, 14331442 (2019).

Article PubMed PubMed Central Google Scholar

Tsai, W. L. E., Schedl, M. E., Maley, J. M. & McCormack, J. E. More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens. Mol. Ecol. Resour. 20, 12201227 (2020).

Article CAS PubMed Google Scholar

Fernndez-Vizarra, E., Enrquez, J. A., Prez-Martos, A., Montoya, J. & Fernndez-Silva, P. Tissue-specific differences in mitochondrial activity and biogenesis. Mitochondrion 11, 207213 (2011).

Article PubMed Google Scholar

Menail, H. A. et al. Flexible thermal sensitivity of mitochondrial oxygen consumption and substrate oxidation in flying insect species. Front. Physiol. 13, 897174 (2022).

Article PubMed PubMed Central Google Scholar

Ferrari, G. et al. Developing the protocol infrastructure for DNA sequencing natural history collections. Biodivers. Data J. 11, 102317 (2023).

Article Google Scholar

Hundsdoerfer, A. & Kitching, I. A method for improving DNA yield from older specimens of large Lepidoptera while minimizing damage to external and internal abdominal characters. Arthropod. Syst. Phylogeny 68, 151155 (2010).

Article Google Scholar

Twort, V. G., Minet, J., Wheat, C. W. & Wahlberg, N. Museomics of a rare taxon: Placing Whalleyanidae in the Lepidoptera Tree of Life. Syst. Entomol. 46, 926937 (2021).

Article Google Scholar

Bhler-Cortesi, T. & Wymann, H. P. Schmetterlinge: Tagfalter Der Schweiz. (Verlag Paul Haupt, 2019).

Smith, A. D. et al. Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing. Sci. Rep. 11, 12635 (2021).

Article CAS PubMed PubMed Central Google Scholar

Gutaker, R. M., Reiter, E., Furtwngler, A., Schuenemann, V. J. & Burbano, H. A. Extraction of ultrashort DNA molecules from herbarium specimens. Biotechniques 62, 7679 (2017).

Article CAS PubMed Google Scholar

Caldern-Corts, N., Quesada, M., Cano-Camacho, H. & Zavala-Pramo, G. A simple and rapid method for DNA isolation from xylophagous insects. Int. J. Mol. Sci. 11, 50565064 (2010).

Article PubMed PubMed Central Google Scholar

Caligiuri, L. G. et al. Optimization of DNA extraction from individual sand flies for PCR amplification. Methods Protoc. 2, 115 (2019).

Article Google Scholar

El-Ashram, S., Al Nasr, I. & Suo, X. Nucleic acid protocols: Extraction and optimization. Biotechnol. Rep. 12, 3339 (2016).

Article Google Scholar

Healey, A., Furtado, A., Cooper, T. & Henry, R. J. Protocol: A simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 10, 21 (2014).

Article PubMed PubMed Central Google Scholar

Poinar, H. N. et al. Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 1979(281), 402406 (1998).

Article ADS Google Scholar

Jaenicke-Desprs, V. et al. Early allelic selection in maize as revealed by ancient DNA. Science 1979(302), 12061208 (2003).

Article ADS Google Scholar

Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. USA 110, 1575815763 (2013).

Article ADS CAS PubMed PubMed Central Google Scholar

Schubert, M. et al. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat. Protoc. 9, 10561082 (2014).

Article CAS PubMed Google Scholar

Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).

Article PubMed PubMed Central Google Scholar

Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 314324 (IEEE, 2019). https://doi.org/10.1109/IPDPS.2019.00041.

Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: Fast processing of NGS alignment formats. Bioinformatics 31, 20322034 (2015).

Article CAS PubMed PubMed Central Google Scholar

Link, V. et al. ATLAS: Analysis tools for low-depth and ancient samples. bioRxiv. https://doi.org/10.1101/105346 (2017).

Jnsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage20: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 16821684 (2013).

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