Interestingly, these regulatory elements were closely linked with the same developmental pathways that allowed for flight-like wing development.
"This work tells us more about the origins of moa and kiwi," explained Otago University's Dr Paul Gardner, who co-authored the study alongside former student Dr Nicole Wheeler.
"It supports the hypothesis that the ancestral moa flew here, while the ancestral kiwi, which is related to the emu may have walked, or indeed flown from the likes of Australia or Madagascar over the ancient Gondwanan continent."
In contrast with previous work, which emphasised changes to protein-coding DNA as driving flightlessness, the new study associated loss of flight more strongly with regulatory evolution in "non-coding" DNA.
The study, led by Harvard University researchers, drew on genetic analyses of kiwi blood samples that were permitted by Ngai Tahu and Te Ati Awa iwi, along with moa and kiwi specimens collected by the late Professor Allan Baker.
"Due to this collaboration, we now have a better idea now that the places of the genome that we concentrate on - the protein-coding gene - may not in fact be the ultimate source of species diversity and change," Gardner said.
Another Otago University researcher who wasn't part of the study, Dr Nic Rawlence, said the evolution and loss of flight in ratites had long fascinated scientists.
"The members of this bird group are descended from flying ancestors that independently lost flight after the extinction of the dinosaurs."
Moa were unique among ratites in that they had no wings left.
"However, the partial moa genome contains most of the functional genes associated with wing development and flight, creating an evolutionary mystery."
The lack of wings wasn't simply a case of gene loss, he said, and the new study may have offered the answer.
"More ratite genomes, especially additional moa and the extinct Madagascan elephant bird, would go a long way to finally resolving this debate," Rawlence said.
"As for the de-extinction of moa, this study just goes to show that having a genome does not mean you can bring back the dead – there's a whole lot of regulation of that genome that you would also have to recreate as well. That's a tough call."
It's the latest instance in which DNA analysis has dramatically changed what we know about many of our native species.
To the relief of those uncomfortable with the thought of our national bird being an Aussie immigrant, a landmark DNA-based study in 2014 found the kiwi was more closely related to the giant Madagascan native.
That same year, insights gleaned from DNA analysis also revealed how the moa was more closely related to South America's tinamous than its old bushmate, the kiwi, and concluded both moa and kiwi separately evolved to become flightless after their ancestors flew here.
