Highly Informative Ancient DNA ‘Snippets’ for New Zealand Moa

<div><h3>Background</h3><p>Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand’s moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species.</p> <h3>Methodology/Principal Findings</h3><p>By targeting such ‘snippets’, we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of <em>Pachyornis geranoides, Dinornis novaezealandiae,</em> and <em>Dinornis robustus</em> were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa <em>Anomalopteryx didiformis</em> and <em>Euryapteryx curtus</em> were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments.</p> <h3>Conclusions/Significance</h3><p>Short highly variable mitochondrial ‘snippets’ allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.</p> </div

Moa D-loop nucleotide variation.

<p>The number of changes was calculated in bins of six nucleotides; shown on the Y axis on the right. Transitions are shown in red, transversions are shown in green. Insertions and deletions are shown by downward and upward pointing arrowheads respectively. Highly-conserved avian F, E, D, C, and E boxes are shown in grey <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050732#pone.0050732-Randi1" target="_blank">[16]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050732#pone.0050732-Ruokonen1" target="_blank">[18]</a>. The regions covered by the HVRI and HVRII are shown as light grey boxes. TAS sequences are in red. Rates of mutation were calculated in bins of 30 nucleotides and are shown as percentage change per million years (%/Myr) on the left Y axis.</p

Location and spanning network analysis of moa haplotypes.

<p>Dots on the map of New Zealand (left) represent sample locations, identified by a unique color code and number (key in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050732#pone.0050732.s002" target="_blank">Figure S2</a>). Sequences were aligned in ClustalW <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050732#pone.0050732-Larkin1" target="_blank">[35]</a>. Haplotype networks (right) were constructed using TCS 1.21 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050732#pone.0050732-Clement1" target="_blank">[31]</a> (with gaps treated as the fifth state) and are coloured according to sample location. Unknown locations are shown by clear circles. Circles are labeled in the network with haplotype number (eg P10 - <i>Pachyornis geranoides</i> haplotype 10). The circle size indicates the frequency of each haplotype; small for 1 occurrence, medium for 2–4, large for 5–10 and the largest circles for more than 10. Lines between haplotypes show single mutation events and linebreaks indicate intermediate, as yet undetected haplotypes. Light grey lines show possible additional linkages.</p

Selected moa bone fragments from Tiniroto swamp.

<p><b>A</b>. A selection of degraded moa bone samples recovered from Tiniroto Swamp. <b>B</b>. and <b>C</b>. Examples of bone fragments successful for aDNA extraction that consisted largely of trabecular material.</p

Moa bone fragments from Tiniroto swamp.

<p>Sample haplotype and sex are shown.</p