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{{short description|Study of genomic data from museum collections}}

'''Museomics''' is the study of [[Genomics|genomic]] data obtained from [[ancient DNA]] (aDNA) and historic DNA (hDNA) specimens in [[museum collections]].<ref name="Raxworthy"/><ref name="Orlando">{{cite journal |last1=Orlando |first1=Ludovic |last2=Cooper |first2=Alan |title=Using Ancient DNA to Understand Evolutionary and Ecological Processes |journal=Annual Review of Ecology, Evolution, and Systematics |date=23 November 2014 |volume=45 |issue=1 |pages=573–598 |doi=10.1146/annurev-ecolsys-120213-091712 |language=en |issn=1543-592X}}</ref>
Early research in this area focused on short sequences of DNA from [[mitochondrial genes]], but sequencing of [[Whole genome sequencing|whole genomes]] has become possible.<ref name="Raxworthy">{{cite journal |last1=Raxworthy |first1=Christopher J. |last2=Smith |first2=Brian Tilston |title=Mining museums for historical DNA: advances and challenges in museomics |journal=Trends in Ecology & Evolution |date=November 2021 |volume=36 |issue=11 |pages=1049–1060 |doi=10.1016/j.tree.2021.07.009 |pmid=34456066 |bibcode=2021TEcoE..36.1049R |s2cid=239687836 |url=https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(21)00214-7.pdf |access-date=27 June 2022}}</ref>
[[Massive parallel sequencing|Next-generation sequencing]] (NGS) and [[high-throughput sequencing]] (HTS) methods can be applied to the analysis of genetic datasets extracted from collections materials.<ref name="Besnard">{{cite journal |last1=Besnard |first1=Guillaume |last2=Christin |first2=Pascal-Antoine |last3=Malé |first3=Pierre-Jean G. |last4=Lhuillier |first4=Emeline |last5=Lauzeral |first5=Christine |last6=Coissac |first6=Eric |last7=Vorontsova |first7=Maria S. |title=From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition |journal=Journal of Experimental Botany |date=1 December 2014 |volume=65 |issue=22 |pages=6711–6721 |doi=10.1093/jxb/eru395 |pmid=25258360 |issn=0022-0957|doi-access=free }}</ref> Such techniques have been described as a "third revolution in sequencing technology".<ref name="van Dijk">{{cite journal |last1=van Dijk |first1=Erwin L. |last2=Jaszczyszyn |first2=Yan |last3=Naquin |first3=Delphine |last4=Thermes |first4=Claude |title=The Third Revolution in Sequencing Technology |journal=Trends in Genetics |date=1 September 2018 |volume=34 |issue=9 |pages=666–681 |doi=10.1016/j.tig.2018.05.008 |pmid=29941292 |s2cid=49408925 |url=https://www.sciencedirect.com/science/article/abs/pii/S0168952518300969 |access-date=27 June 2022 |language=en |issn=0168-9525|url-access=subscription }}</ref> 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]].<ref name="Callaway">{{cite journal |last1=Callaway |first1=Ewen |title=Divided by DNA: The uneasy relationship between archaeology and ancient genomics |journal=Nature |date=28 March 2018 |volume=555 |issue=7698 |pages=573–576 |doi=10.1038/d41586-018-03773-6 |bibcode=2018Natur.555..573C |language=en|doi-access=free }}</ref><ref name="Dance">{{cite journal |last1=Dance |first1=Amber |title=The tale of the domesticated horse |journal=Knowable Magazine |date=4 May 2022 |doi=10.1146/knowable-050422-1 |doi-access=free |url=https://knowablemagazine.org/article/living-world/2022/tale-domesticated-horse |access-date=18 May 2022|url-access=subscription }}</ref>

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 [[Migration (ecology)|migrations]].<ref name="Bi"/><ref name="Strijk">{{cite journal |last1=Strijk |first1=Joeri S. |last2=Binh |first2=Hoàng Thi |last3=Ngoc |first3=Nguyen Van |last4=Pereira |first4=Joan T. |last5=Slik |first5=J. W. Ferry |last6=Sukri |first6=Rahayu S. |last7=Suyama |first7=Yoshihisa |last8=Tagane |first8=Shuichiro |last9=Wieringa |first9=Jan J. |last10=Yahara |first10=Tetsukazu |last11=Hinsinger |first11=Damien D. |title=Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea |journal=PLOS ONE |date=22 May 2020 |volume=15 |issue=5 |article-number=e0232936 |doi=10.1371/journal.pone.0232936 |pmid=32442164 |pmc=7244142 |bibcode=2020PLoSO..1532936S |language=en |issn=1932-6203|doi-access=free }}</ref><ref name="Moreno-Aguilar">{{cite journal |last1=Moreno-Aguilar |first1=María Fernanda |last2=Arnelas |first2=Itziar |last3=Sánchez-Rodríguez |first3=Aminael |last4=Viruel |first4=Juan |last5=Catalán |first5=Pilar |title=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 |journal=Frontiers in Plant Science |date=2020 |volume=11 |page=819 |doi=10.3389/fpls.2020.00819 |pmid=32754167 |pmc=7333454 |issn=1664-462X|doi-access=free |bibcode=2020FrPS...11..819M }}</ref> Research may be used to identify isolated populations and inform conservation priorities.<ref name="Orlando"/>

However, museum specimens can be poorly preserved and are subject to degradation<ref name="Bi"/> and contamination.<ref name="Orlando"/><ref name="Guschanski">{{cite journal |last1=Guschanski |first1=Katerina |last2=Krause |first2=Johannes |last3=Sawyer |first3=Susanna |last4=Valente |first4=Luis M. |last5=Bailey |first5=Sebastian |last6=Finstermeier |first6=Knut |last7=Sabin |first7=Richard |last8=Gilissen |first8=Emmanuel |last9=Sonet |first9=Gontran |last10=Nagy |first10=Zoltán T. |last11=Lenglet |first11=Georges |last12=Mayer |first12=Frieder |last13=Savolainen |first13=Vincent |title=Next-Generation Museomics Disentangles One of the Largest Primate Radiations |journal=Systematic Biology |date=1 July 2013 |volume=62 |issue=4 |pages=539–554 |doi=10.1093/sysbio/syt018 |pmid=23503595 |pmc=3676678 |url=https://academic.oup.com/sysbio/article/62/4/539/1611933 |access-date=28 June 2022 |issn=1063-5157}}</ref> 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. [[Polymerase chain reaction|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.<ref name="Bi">{{cite journal |last1=Bi |first1=Ke |last2=Linderoth |first2=Tyler |last3=Vanderpool |first3=Dan |last4=Good |first4=Jeffrey M. |last5=Nielsen |first5=Rasmus |last6=Moritz |first6=Craig |title=Unlocking the vault: next-generation museum population genomics |journal=Molecular Ecology |date=December 2013 |volume=22 |issue=24 |pages=6018–6032 |doi=10.1111/mec.12516 |pmid=24118668 |pmc=4134471 |bibcode=2013MolEc..22.6018B |language=en}}</ref> Optimal methods for working with hDNA and aDNA can differ as a result of differences in their DNA degradation history.<ref name="Raxworthy"/>

Museomics also involves destructive sampling, irreversibly removing parts of sometimes rare specimens to obtain DNA.<ref>{{CiteQ|Q106839643}}</ref> This can be contentious for curators and collection staff,<ref name="Raxworthy"/> 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.<ref name="Sawchuk">{{cite news |last1=Sawchuk |first1=Elizabeth |last2=Prendergast |first2=Mary |title=Ancient DNA is a powerful tool for studying the past – when archaeologists and geneticists work together |url=https://theconversation.com/ancient-dna-is-a-powerful-tool-for-studying-the-past-when-archaeologists-and-geneticists-work-together-111127 |access-date=27 June 2022 |work=The Conversation |date=March 11, 2019 |language=en}}</ref><ref name="Card">{{cite journal |last1=Card |first1=Daren C. |last2=Shapiro |first2=Beth |last3=Giribet |first3=Gonzalo |last4=Moritz |first4=Craig |last5=Edwards |first5=Scott V. |title=Museum Genomics |journal=Annual Review of Genetics |date=23 November 2021 |volume=55 |issue=1 |pages=633–659 |doi=10.1146/annurev-genet-071719-020506 |pmid=34555285 |s2cid=237616302 |language=en |issn=0066-4197|doi-access=free }}</ref>

==See also==
*[[Genomics]]
*[[Proteomics]]
*[[List of omics topics in biology]]

== References ==
{{reflist}}

{{Archaeology}}
{{Genetics}}
{{Portal bar|Evolutionary biology|Paleontology}}

[[Category:Museology]]
[[Category:DNA]]
[[Category:Genetics]]
[[Category:Genetic genealogy]]
[[Category:Methods in archaeology]]
[[Category:Ancient DNA (human)]]
[[Category:Analytical chemistry]]
[[Category:Omics]]

Museomics - История изменений

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