دورية أكاديمية
أعرض في EDS

Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.

التفاصيل البيبلوغرافية
العنوان: Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.
المؤلفون: Derkarabetian S; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA., Benavides LR; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA., Giribet G; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
المصدر: Molecular ecology resources [Mol Ecol Resour] 2019 Nov; Vol. 19 (6), pp. 1531-1544. Date of Electronic Publication: 2019 Sep 18.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford, England : Blackwell
مواضيع طبية MeSH: Birds/*genetics , Preservation, Biological/*methods , Sequence Analysis, DNA/*methods, Animals ; Biodiversity ; DNA/genetics ; Ethanol/chemistry ; Formaldehyde/chemistry ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Insecta ; Mitochondria/genetics ; Museums ; Phylogeny ; Specimen Handling/methods
مستخلص: Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of "fresh" specimens preserved in >95% ethanol and stored at -80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%-80% ethanol and stored at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol-preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off-target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.
(© 2019 John Wiley & Sons Ltd.)
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معلومات مُعتمدة: Harvard Dean's Fund; DEB-1601208 Division of Environmental Biology; DEB-1754278 Division of Environmental Biology
فهرسة مساهمة: Keywords: Opiliones; degraded DNA; ethanol preservation; museum collections; phylogenomics; ultraconserved elements
المشرفين على المادة: 1HG84L3525 (Formaldehyde)
3K9958V90M (Ethanol)
9007-49-2 (DNA)
تواريخ الأحداث: Date Created: 20190827 Date Completed: 20200312 Latest Revision: 20200312
رمز التحديث: 20231215
DOI: 10.1111/1755-0998.13072
PMID: 31448547
قاعدة البيانات: MEDLINE
الوصف
تدمد:1755-0998
DOI:10.1111/1755-0998.13072