Moa Genome Sequencing

Objective

To create the most detailed moa genome possible in order to advance our understanding of one of the most iconic birds that ever lived.

Attempt 3 - Jul. 2016

Negative result. Endogenous DNA content not high enough to proceed.  We did however obtain some poor quality moa sequences which are informing our research.

Samples Summary

2 pieces are cut off larger bones and, when cut, smelt very high in endogenous protein

  • WD1 Phalange Euryapteryx
  • WD2 Rib Dinornis
  • WD3 Sternal rib Dinornis
  • WD4 Femur Dinornis (cut piece)
  • WD5 Tibia Euryapteryx (cut piece)

UCSC Analysis

I just uploaded a spreadsheet containing the sequencing summaries for the five new Moa samples. These samples seem to have very similar DNA preservation compared to the other batches. The best sample seems to be WD3 which was estimated to contain 1.9% endogenous DNA and has the characteristics of ancient DNA such as a short mean fragment length and damaged ends. The Kiwi reference genome is distant and isn't perfect so the endogenous percentage may be higher than 1.9 but it's difficult to say by how much.

 

Attempt 2 - Feb. 2016

Negative result. Endogenous DNA content not high enough to proceed.

Samples Summary

4 samples today – each is from an individual bird so they should not be pooled. All individuals are collected from Pyramid Valley in North Canterbury a site that has excellent DNA preservation - each is from a robust piece of the shaft of a long bone. IDs may not be 100% accurate but are based on size and what is known from the site.

UCSC Analysis

Just just completed the analysis of the last four samples. These are better preserved than the previous samples, but still pretty poor. The best two samples are only around 1.5% endogenous DNA (so 98.5% environmental DNA), which would make it a very expensive genome sequencing project. My recommendation would be to keep looking for a well preserved bone.

I attach the report that details the results. We did not sequence sufficiently deeply to do any analysis; we simply tested the overall preservation of the bones.

 

Attempt 1 - Oct. 2015

Negative result. Endogenous DNA content not high enough to proceed.

Samples Summary

251g of powdered bone. Dinornis robustus Tibiotarsus – age C 1500ybp taken from an excavation in Rosslea, North Canterbury, March 2015.

UCSC Analysis

We extracted only one sample (and one blank) as a first pass. We sequenced about 4 million reads, of which 99.8% were unique (which means the library was very complex, or that a lot of different DNA sequences were present in the extract). Unfortunately, only 0.04% of these mapped to the Tinamou genome, which is approximately the same proportion that mapped to human. We also attempted to map the reads to the Anomalopteryx didiformis mitochondrial genome, and recovered only a few reads (0.014X coverage). A comparison to all data available online using the software MEGAN indicated that 84% of the recovered reads mapped to bacteria.

In summary, this specimen appears to have a very high bacterial component. It is not really possible to tell at this coverage whether there is also lots of moa DNA, but the enormous complexity of bacterial sequences means that ~99% of the recovered data will have to be thrown away.

If you want us to repeat the process or to sequence the sample more deeply (to see if we can learn whether there are lots of molecules of moa DNA present) we will. However, it might be better to attempt this with a better preserved bone at this point -- one where the proportion of moa DNA to bacterial DNA is skewed more in favor of moa.