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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
Published on: November 30, 2021
Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna--protocols, problems, and
Morten E Allentoft1, Charlotte Oskam, Jayne Houston
1Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia. morten.allentoft@gmail.com
Plos One
|February 10, 2011
Summary
Researchers developed new microsatellite markers for studying extinct New Zealand moa. This ancient DNA (aDNA) method overcomes challenges with low copy number DNA, enabling genetic diversity studies beyond mitochondrial DNA.
Area of Science:
- Paleogenomics
- Molecular Evolution
- Ancient DNA Technology
Background:
- Microsatellite analysis is widely used for extant species but challenging for low copy number (LCN) DNA found in ancient samples.
- Current ancient DNA research heavily relies on mitochondrial DNA, limiting the scope of genetic studies.
- Developing new molecular markers is crucial for advancing the field of paleogenomics.
Purpose of the Study:
- To develop and validate novel microsatellite markers specifically for the extinct New Zealand moa (Dinornithiformes).
- To establish protocols for reliable microsatellite analysis on ancient DNA (aDNA) with low template quantities.
- To enable broader genetic diversity studies of extinct taxa beyond mitochondrial DNA analysis.
Main Methods:
- High-throughput sequencing (GS-FLX) was used to identify candidate microsatellite loci from fossil moa bone and eggshell DNA.
- >60 primer pairs were designed and tested on DNA from Dinornis robustus specimens.
- Allelic dropout rates were quantified, and criteria were established to maximize data fidelity in ancient DNA samples.
Main Results:
- Six polymorphic microsatellite loci were successfully characterized in the extinct moa.
- Despite challenges with allelic dropout (36-70% PCR reactions), a robust methodology was developed.
- A comprehensive microsatellite dataset was generated for 74 moa individuals (600-5000 years old) with an 84% success rate.
Conclusions:
- The developed microsatellite markers and protocols are effective for studying the genetics of extinct moa populations.
- This methodology provides a framework for applying microsatellite analysis to ancient DNA samples of unprecedented age.
- The study significantly expands the toolkit for ancient DNA research, moving beyond mitochondrial DNA limitations.
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