Museomics

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Museomics is the study of genomic data obtained from ancient DNA (aDNA) and historic DNA (hDNA) specimens in museum collections. [1] [2] Early research in this area focused on short sequences of DNA from mitochondrial genes, but sequencing of whole genomes has become possible. [1] Next-generation sequencing (NGS) and high-throughput sequencing (HTS) methods can be applied to the analysis of genetic datasets extracted from collections materials. [3] Such techniques have been described as a "third revolution in sequencing technology". [4] Like radiocarbon dating, the techniques of museomics are a transformative technology. Results are revising and sometimes overturning previously accepted theories about a wide variety of topics such as the domestication of the horse. [5] [6]

Museum collections contain unique resources such as natural history specimens, which can be used for genome-scale examinations of species, their evolution, and their responses to environmental change. Ancient DNA provides a unique window into genetic change over time. It enables scientists to directly study evolutionary and ecological processes, comparing ancient and modern populations, identifying distinct populations, and revealing patterns of change such as extinctions and migrations. [7] [8] [9] Research may be used to identify isolated populations and inform conservation priorities. [2]

However, museum specimens can be poorly preserved and are subject to degradation [7] and contamination. [2] [10] Genomic analyses face considerable challenges as a result of the highly degraded DNA typical of museum specimens. DNA from such samples is often subject to post-mortem nucleotide damage such as the hydrolytic deamination of cytosine (C) to uracil (U) residues. PCR amplification of damaged templates can further substitute uracils with thymine (T), completing a C to T substitution path. Such errors tend to occur towards the ends of molecules, accumulate with time, and can be significant in specimens a century-old or later. Robust genomic and statistical techniques are needed to rigorously detect and avoid errors and genotyping uncertainties when carrying out analyses based on museum collections. [7] Optimal methods for working with hDNA and aDNA can differ as a result of differences in their DNA degradation history. [1]

Museomics also involves destructive sampling, irreversibly removing parts of sometimes rare specimens to obtain DNA. [11] This can be contentious for curators and collection staff, [1] involving a variety of ethical issues around the handling and destruction of objects, colonial acquisition and repatriation practices, and present-day social and political implications of research. Museums, universities and journals are increasingly developing ethics statements, best practices and guidelines for such work. [12] [13]

See also

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References

  1. 1 2 3 4 Raxworthy, Christopher J.; Smith, Brian Tilston (November 2021). "Mining museums for historical DNA: advances and challenges in museomics" (PDF). Trends in Ecology & Evolution. 36 (11): 1049–1060. doi:10.1016/j.tree.2021.07.009. PMID   34456066. S2CID   239687836 . Retrieved 27 June 2022.
  2. 1 2 3 Orlando, Ludovic; Cooper, Alan (23 November 2014). "Using Ancient DNA to Understand Evolutionary and Ecological Processes". Annual Review of Ecology, Evolution, and Systematics. 45 (1): 573–598. doi:10.1146/annurev-ecolsys-120213-091712. ISSN   1543-592X . Retrieved 27 June 2022.
  3. ↑ Besnard, Guillaume; Christin, Pascal-Antoine; Malé, Pierre-Jean G.; Lhuillier, Emeline; Lauzeral, Christine; Coissac, Eric; Vorontsova, Maria S. (1 December 2014). "From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition". Journal of Experimental Botany. 65 (22): 6711–6721. doi: 10.1093/jxb/eru395 . ISSN   0022-0957. PMID   25258360.
  4. ↑ van Dijk, Erwin L.; Jaszczyszyn, Yan; Naquin, Delphine; Thermes, Claude (1 September 2018). "The Third Revolution in Sequencing Technology". Trends in Genetics. 34 (9): 666–681. doi:10.1016/j.tig.2018.05.008. ISSN   0168-9525. PMID   29941292. S2CID   49408925 . Retrieved 27 June 2022.
  5. ↑ Callaway, Ewen (28 March 2018). "Divided by DNA: The uneasy relationship between archaeology and ancient genomics". Nature. 555 (7698): 573–576. Bibcode:2018Natur.555..573C. doi: 10.1038/d41586-018-03773-6 .
  6. ↑ Dance, Amber (4 May 2022). "The tale of the domesticated horse". Knowable Magazine. doi:10.1146/knowable-050422-1 . Retrieved 18 May 2022.
  7. 1 2 3 Bi, Ke; Linderoth, Tyler; Vanderpool, Dan; Good, Jeffrey M.; Nielsen, Rasmus; Moritz, Craig (December 2013). "Unlocking the vault: next-generation museum population genomics". Molecular Ecology. 22 (24): 6018–6032. doi:10.1111/mec.12516. PMC   4134471 . PMID   24118668 . Retrieved 27 June 2022.
  8. ↑ Strijk, Joeri S.; Binh, Hoàng Thi; Ngoc, Nguyen Van; Pereira, Joan T.; Slik, J. W. Ferry; Sukri, Rahayu S.; Suyama, Yoshihisa; Tagane, Shuichiro; Wieringa, Jan J.; Yahara, Tetsukazu; Hinsinger, Damien D. (22 May 2020). "Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea". PLOS ONE. 15 (5): e0232936. Bibcode:2020PLoSO..1532936S. doi: 10.1371/journal.pone.0232936 . ISSN   1932-6203. PMC   7244142 . PMID   32442164.
  9. ↑ Moreno-Aguilar, María Fernanda; Arnelas, Itziar; Sánchez-Rodríguez, Aminael; Viruel, Juan; Catalán, Pilar (2020). "Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago Megalachne and Podophorus Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues". Frontiers in Plant Science. 11: 819. doi: 10.3389/fpls.2020.00819 . ISSN   1664-462X. PMC   7333454 . PMID   32754167.
  10. ↑ Guschanski, Katerina; Krause, Johannes; Sawyer, Susanna; Valente, Luis M.; Bailey, Sebastian; Finstermeier, Knut; Sabin, Richard; Gilissen, Emmanuel; Sonet, Gontran; Nagy, Zoltán T.; Lenglet, Georges; Mayer, Frieder; Savolainen, Vincent (1 July 2013). "Next-Generation Museomics Disentangles One of the Largest Primate Radiations". Systematic Biology. 62 (4): 539–554. doi:10.1093/sysbio/syt018. ISSN   1063-5157. PMC   3676678 . PMID   23503595 . Retrieved 28 June 2022.
  11. ↑ Lara Dawn Shepherd; Matt Hendrik Buys; Carlos A. Lehnebach; Antony Kusabs; Leon Perrie (2020). "Do herbarium specimens collected by Banks and Solander during Cook's voyage around New Zealand in 1769-70 contain DNA?". Tuhinga: Records of the Museum of New Zealand Te Papa Tongarewa. Te Papa. 31: 113–119. ISSN   1173-4337. Wikidata   Q106839643.
  12. ↑ Sawchuk, Elizabeth; Prendergast, Mary (March 11, 2019). "Ancient DNA is a powerful tool for studying the past – when archaeologists and geneticists work together". The Conversation. Retrieved 27 June 2022.
  13. ↑ Card, Daren C.; Shapiro, Beth; Giribet, Gonzalo; Moritz, Craig; Edwards, Scott V. (23 November 2021). "Museum Genomics". Annual Review of Genetics. 55 (1): 633–659. doi: 10.1146/annurev-genet-071719-020506 . ISSN   0066-4197. PMID   34555285. S2CID   237616302 . Retrieved 27 June 2022.
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