Squeezing water from a stone: High-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

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1 Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States
2 Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States
3 Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California, United States
4 Entomology Department, California Academy of Sciences, San Francisco, California, United States
5 Department of Biomolecular Engineering and Bioinformatics, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States
6 Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
7 Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, United States
8 Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States
9 Museum Zoologicum Bogoriense (MZB), Indonesia Institute of Sciences (LIPI), Cibinong, West Java, Indonesia
10 Department of Life Sciences, The Natural History Museum, London, London, United Kingdom
11 School of Life Sciences and Technology, Institute of Technology Bandung, Bandung, West Java, Indonesia
DOI
10.7287/peerj.preprints.26466v1
Published
Accepted
Subject Areas
Genetics, Genomics, Taxonomy, Zoology
Keywords
Draco, formalin-fixation, ancient DNA, phylogeny, taxonomy
Copyright
© 2018 McGuire et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
McGuire JA, Cotoras DD, O'Connell B, Lawalata SZS, Wang-Claypool CY, Stubbs A, Huang X, Wogan GOU, Hykin SM, Reilly SB, Bi K, Riyanto A, Arida E, Smith LL, Milne H, Streicher JW, Iskandar DT. 2018. Squeezing water from a stone: High-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards. PeerJ Preprints 6:e26466v1

Abstract

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (547 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

ND2 sequence data for members of the Draco fimbriatus group plus 13 mitochondrial sequence reads obtained from the D. cristatellus holotype

This file includes ND2 sequence data obtained via traditional Sanger sequencing for 39 individuals representing Draco cristatellus, D. fimbriatus, D. hennigi, D. punctatus, and D. maculatus, plus 183 base pairs of ND2 obtained via MiSeq HTS for the Draco cristatellus holotype (BMNH 1872.2.19.4). In addition, the 13 mitochondrial sequence reads obtained for the D. cristatellus holotype are provided.

DOI: 10.7287/peerj.preprints.26466v1/supp-1