Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards
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 spec...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
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PeerJ Inc.
2018-03-01
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| Online Access: | https://peerj.com/articles/4470.pdf |
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| author | Jimmy A. McGuire Darko D. Cotoras Brendan O’Connell Shobi Z.S. Lawalata Cynthia Y. Wang-Claypool Alexander Stubbs Xiaoting Huang Guinevere O.U. Wogan Sarah M. Hykin Sean B. Reilly Ke Bi Awal Riyanto Evy Arida Lydia L. Smith Heather Milne Jeffrey W. Streicher Djoko T. Iskandar |
| author_facet | Jimmy A. McGuire Darko D. Cotoras Brendan O’Connell Shobi Z.S. Lawalata Cynthia Y. Wang-Claypool Alexander Stubbs Xiaoting Huang Guinevere O.U. Wogan Sarah M. Hykin Sean B. Reilly Ke Bi Awal Riyanto Evy Arida Lydia L. Smith Heather Milne Jeffrey W. Streicher Djoko T. Iskandar |
| author_sort | Jimmy A. McGuire |
| collection | DOAJ |
| description | 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 (721 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. |
| first_indexed | 2024-03-09T06:57:57Z |
| format | Article |
| id | doaj.art-3a59d0e85b9b465f8df3138b38e8ee55 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:57:57Z |
| publishDate | 2018-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-3a59d0e85b9b465f8df3138b38e8ee552023-12-03T09:59:19ZengPeerJ Inc.PeerJ2167-83592018-03-016e447010.7717/peerj.4470Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizardsJimmy A. McGuire0Darko D. Cotoras1Brendan O’Connell2Shobi Z.S. Lawalata3Cynthia Y. Wang-Claypool4Alexander Stubbs5Xiaoting Huang6Guinevere O.U. Wogan7Sarah M. Hykin8Sean B. Reilly9Ke Bi10Awal Riyanto11Evy Arida12Lydia L. Smith13Heather Milne14Jeffrey W. Streicher15Djoko T. Iskandar16Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaDepartment of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States of AmericaDepartment of Biomolecular Engineering and Bioinformatics, Baskin School of Engineering, University of California, Santa Cruz, CA, United States of AmericaMuseum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaMuseum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaMuseum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaKey Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, ChinaDepartment of Environmental Science, Policy, and Management, University of California, Berkeley, CA, United States of AmericaMuseum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaMuseum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaComputational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States of AmericaMuseum Zoologicum Bogoriense, Research Center for Biology-The Indonesian Institute of Sciences, Cibinong, IndonesiaMuseum Zoologicum Bogoriense, Research Center for Biology-The Indonesian Institute of Sciences, Cibinong, IndonesiaMuseum of Vertebrate Zoology, University of California, Berkeley, CA, United States of AmericaDepartment of Biomolecular Engineering and Bioinformatics, Baskin School of Engineering, University of California, Santa Cruz, CA, United States of AmericaDepartment of Life Sciences, The Natural History Museum, London, United KingdomSchool of Life Sciences and Technology, Institute of Technology Bandung, Bandung, West Java, IndonesiaWe 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 (721 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.https://peerj.com/articles/4470.pdfDracoFormalin-fixationAncient DNAPhylogenyTaxonomy |
| spellingShingle | Jimmy A. McGuire Darko D. Cotoras Brendan O’Connell Shobi Z.S. Lawalata Cynthia Y. Wang-Claypool Alexander Stubbs Xiaoting Huang Guinevere O.U. Wogan Sarah M. Hykin Sean B. Reilly Ke Bi Awal Riyanto Evy Arida Lydia L. Smith Heather Milne Jeffrey W. Streicher Djoko T. Iskandar Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards PeerJ Draco Formalin-fixation Ancient DNA Phylogeny Taxonomy |
| title | Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards |
| title_full | Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards |
| title_fullStr | Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards |
| title_full_unstemmed | Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards |
| title_short | Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards |
| title_sort | squeezing water from a stone high throughput sequencing from a 145 year old holotype resolves barely a cryptic species problem in flying lizards |
| topic | Draco Formalin-fixation Ancient DNA Phylogeny Taxonomy |
| url | https://peerj.com/articles/4470.pdf |
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