To create the most detailed moa genome possible in order to advance our understanding of one of the most iconic birds that ever lived.
David is a citizen/wannabe scientist helping to advance the scientific techniques required to prevent species extinction through genetic intervention. He's the founder of The Genetic Rescue Foundation a not-for-profit venture that leverages the power of new platforms for collaboration like Experiment and Science Exchange to fund and complete research.
The Paleogenomics Lab is a joint venture between two PIs: Beth Shapiro, and Richard (Ed) Green. Their research focuses on a wide range of evolutionary and ecological questions, mostly involving the application of genomics techniques to better understand how species and populations evolve through time.
Initial fundraising for moa genome sequencing was a complete success. Thanks to the support of our contributors our genome sequencing project is currently in progress.View Crowdfunding Campaign
Moa were a family of giant flightless ratites unique to New Zealand. We don’t know exactly when moa’s ancestors got to ancient Zealandia but we know that it was more than 12 million years ago because fossils have been found of moa eggshell from miocene lake deposits. If they were already a large flightless bird then, it means that they may be one of the most ancient inhabitants of NZ. Moa were so unique that there is no closely related species alive today and our entire plant ecosystem was adapted to having moa as the apex browser. This was until the arrival of the first humans around 700 years ago who misjudged the fragility of the ecosystem resulting in one of the worst environmental catastrophes in human history. Hunting and land clearance triggered a moa population collapse and all 13 species of moa were extinct by 400-500 years ago at the latest. We don’t know exactly what impact moa had on the ecosystem but many species moa ate are now themselves critically endangered. It is quite likely moa played an important role in seed dispersal, fire risk mitigation through browsing and nutrient flux.
Moa were an important component of the New Zealand ecosystem and their restoration is an important step in restoring the human damage to our ecosystem. An important feature of moa which makes them a good candidate for de-extinction is their large heavy bones which have preserved DNA better than the bones of smaller animals. Thanks to the work of Allison Cloutier, we now have a near complete genome of the little bush moa. Further expanding our knowledge of this family of birds will revolutionise our understanding of New Zealand’s ecosystem. What’s more, the technology we develop will be directly applicable to countless other restoration projects around the world including those affecting living species like the kakapo.
2 pieces are cut off larger bones and, when cut, smelt very high in endogenous protein
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.
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.
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.
251g of powdered bone. Dinornis robustus Tibiotarsus – age C 1500ybp taken from an excavation in Rosslea, North Canterbury, March 2015.
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.