Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens
Ruane, Sara, Louisiana State University of Alexandria
Austin, Christopher C., Louisiana State University of Alexandria
Published Jan 23, 2017 on Dryad.
Cite this dataset
Ruane, Sara; Austin, Christopher C. (2017). Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens [Dataset]. Dryad. https://doi.org/10.5061/dryad.cm28r
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 (x̄ = 2,318 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.
Includes the 50% missing data alignment/resulting tree and the 35% missing data (i.e., 65% complete) alignment/resulting tree .
Extraction protocol followed in the manuscript.
The assembled contigs for each sequenced individual from Abyss, including the negative control.
Tab delimited text files with information for resulting UCE loci for both the 50% missing data matrix and the 35% missing data matrix (i.e., 65% complete).
Excel file (with two tabs) with details on specimens and library prep information.