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Abstract The use of gDNAs isolated from museum specimens for high throughput sequencing, especially targeted sequencing in the context of phylogenetics, is a common practice. Yet, little understanding has been focused on comparing the quality of DNA and results of sequencing museum DNAs. Dragonflies and damselflies are ubiquitous in freshwater ecosystems and are commonly collected and preserved insects in museum collections hence their use in this study. However, the history of odonate preservation across time and museums has resulted in wide variability in the success of viable DNA extraction, necessitating an assessment of their usefulness in genetic studies. Using Anchored Hybrid Enrichment probes, we sequenced DNA from samples at 2 museums, 48 from the American Museum of Natural History (AMNH) in NYC, USA and 46 from the Naturalis Biodiversity Center (RMNH) in Leiden, Netherlands ranging from global collection localities and across a 120-year time span. We recovered at least 4 loci out of an >1,000 locus probe set for all samples, with the average capture being ~385 loci (539 loci on average when a clade of ambiguous taxa omitted). Neither specimen age nor size was a good predictor of locus capture, but recapture rates differed significantly between museums. Samples from the AMNH had lower overall locus capture than the RMNH, perhaps due to differences in specimen storage over time.
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Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections
Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops . Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops , and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes . A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA. Life Science Identifier ( Hydrablabes periops ) urn:lsid:zoobank.org :pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.
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- Award ID(s):
- 2224119
- PAR ID:
- 10392384
- Date Published:
- Journal Name:
- Frontiers in Ecology and Evolution
- Volume:
- 10
- ISSN:
- 2296-701X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fevo.2022.893088
