dc.creator | Hawkins, Melissa T. R. | es |
dc.creator | Flores, Mary Faith C. | es |
dc.creator | McGowen, Michael | es |
dc.creator | Hinckley Boned, Arlo | es |
dc.date.accessioned | 2023-06-13T10:46:54Z | |
dc.date.available | 2023-06-13T10:46:54Z | |
dc.date.issued | 2022 | |
dc.identifier.citation | Hawkins, M.T.R., Flores, M.F.C., McGowen, M. y Hinclkey Boned, A.D. (2022). A comparative analysis of extraction protocol performance on degraded mammalian museum specimens. Frontiers in Ecology and Evolution, 10, 984056. https://doi.org/10.3389/fevo.2022.984056. | |
dc.identifier.issn | 2296-701X | es |
dc.identifier.uri | https://hdl.handle.net/11441/147161 | |
dc.description.abstract | The extraction of nucleic acids is one of the most routine procedures
used in molecular biology laboratories, yet kit performance may influence
the downstream processing of samples, particularly for samples which are
degraded, and in low concentrations. Here we tested several commercial kits
for specific use on commonly sampled mammalian museum specimens to
evaluate the yield, size distribution, and endogenous content. Samples were
weighed and had approximately equal input material for each extraction.
These sample types are typical of natural history repositories ranged
from 53 to 130 years old. The tested protocols spanned spin-column
based extractions, magnetic bead purification, phenol/chloroform isolation,
and specific modifications for ancient DNA. Diverse types of mammalian
specimens were tested including adherent osteological material, bone and
teeth, skin, and baleen. The concentration of DNA was quantified via
fluorometry, and the size distributions of extracts visualized on an Agilent
TapeStation. Overall, when DNA isolation was successful, all methods
had quantifiable concentrations, albeit with variation across extracts. The
length distributions varied based on the extraction protocol used. Shotgun
sequencing was performed to evaluate if the extraction methods influenced
the amount of endogenous versus exogenous content. The DNA content
was similar across extraction methods indicating no obvious biases for DNA
derived from different sources. Qiagen kits and phenol/chloroform isolation
outperformed the Zymo magnetic bead isolations in these types of samples.
Statistical analyses revealed that extraction method only explained 5% of
the observed variation, and that specimen age explained variation (29%)
more effectively. | es |
dc.format | application/pdf | es |
dc.format.extent | 10 p. | es |
dc.language.iso | eng | es |
dc.publisher | Frontiers Media | es |
dc.relation.ispartof | Frontiers in Ecology and Evolution, 10, 984056. | |
dc.rights | Atribución 4.0 Internacional | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject | museomics | es |
dc.subject | degraded DNA | es |
dc.subject | high throughput sequencing | es |
dc.subject | bone | es |
dc.subject | skin | es |
dc.subject | baleen | es |
dc.subject | osteological tissue | es |
dc.title | A comparative analysis of extraction protocol performance on degraded mammalian museum specimens | es |
dc.type | info:eu-repo/semantics/article | es |
dcterms.identifier | https://ror.org/03yxnpp24 | |
dc.type.version | info:eu-repo/semantics/publishedVersion | es |
dc.rights.accessRights | info:eu-repo/semantics/openAccess | es |
dc.contributor.affiliation | Universidad de Sevilla. Departamento de Zoología | es |
dc.relation.publisherversion | https://doi.org/10.3389/fevo.2022.984056 | es |
dc.identifier.doi | 10.3389/fevo.2022.984056 | es |
dc.journaltitle | Frontiers in Ecology and Evolution | es |
dc.publication.volumen | 10 | es |
dc.publication.initialPage | 984056 | es |