title: Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens.
abstract: Museum specimens provide a wealth of information to biologists, but obtaining genetic data from formalin-fixed and fluid-preserved specimens remains challenging. While DNA sequences have been recovered from such specimens, most approaches are time-consuming and produce low data quality and quantity. Here, we use a modified DNA extraction protocol combined with high-throughput sequencing to recover DNA from formalin-fixed and fluid-preserved snakes that were collected over a century ago and for which little or no modern genetic materials exist in public collections. We successfully extracted DNA and sequenced ultraconserved elements (x¯ = 2318 loci) from 10 fluid-preserved snakes and included them in a phylogeny with modern samples. This phylogeny demonstrates the general use of such specimens in phylogenomic studies and provides evidence for the placement of enigmatic snakes, such as the rare and never-before sequenced Indian Xylophis stenorhynchus. Our study emphasizes the relevance of museum collections in modern research and simultaneously provides a protocol that may prove useful for specimens that have been previously intractable for DNA sequencing.
authors.affiliation: Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA.
authors.forename: Sara
authors.identifier: http://orcid.org/0000-0002-9543-1297
authors.initials: S
authors.lastname: Ruane
authors.affiliation: Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA.|Department of Biological Sciences, Louisiana State University, 202 Life Science Building, 119 Foster Hall, Baton Rouge, LA, 70803, USA.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Austin
mesh_terms: D000818:Animals; D000071298:Body Remains; D004247:DNA / Q000302:isolation & purification*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D005404:Fixatives; D005557:Formaldehyde; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009144:Museums; D010802:Phylogeny; D011309:Preservation, Biological; D012911:Snakes
chemical_list: D005404:Fixatives; D005557:Formaldehyde; D004247:DNA
keywords: museum collections; next-generation sequencing; phylogeny; sequence capture; snakes; ultraconserved elements