Genetic time travel with three enigmatic bird species from New Zealand

What can ancient DNA tell us about the evolutionary history of these birds?

I love a good time travel story, such as Back to the Future, Interstellar or the Terminator movies. Recently, I picked up Julian May’s Saga of the Pliocene Exile, a book series in which a group of 22nd-century outcasts escape their present by stepping through a time-portal into Earth’s Pliocene epoch (between 5 and 2.5 million years ago). Of course, real time travel remains beyond our reach, and reviving extinct species is still more hype than reality (despite dubious claims from the biotech company Colossal Biosciences, see this blog post). However, we’re not entirely without options: by analyzing genetic data, we can reconstruct events in the distant past and still experience some form of scientific time travel.

In this blog post, we will journey to New Zealand to trace the evolutionary stories of three remarkable birds: two extinct species – the Eastern Moa (Emeus crassus) and the Moho (Porphyrio mantelli) – and one survivor – the South Island Takahē (Porphyrio hochstetteri) – which is now clinging on as a relict population. What insights can genetic data reveal about their deep evolutionary past?

The Story of the Eastern Moa

Let’s begin with the Eastern Moa, a giant flightless bird that disappeared around the year 1400. Alexander Verry and his colleagues extracted DNA from museum specimens and sequenced the mitochondrial genomes of 46 individuals to reconstruct its evolutionary history. Their findings suggest that Eastern Moa endured the climate shifts of the Pleistocene within a single refugium, from which it later expanded after the Last Glacial Maximum.

Several lines of evidence support this scenario. First, the mitochondrial DNA revealed no deeply divergent lineages, indicating survival in one refugium rather than several. Second, samples from the proposed refugial area contained the highest levels of genetic diversity, which is a hallmark of long-term persistence. As populations spread into new regions, diversity typically declines, only to rise again as their numbers grow. Consistent with this pattern, the researchers observed a clear increase in genetic diversity when comparing Pleistocene and Holocene samples.

A map of the South Island of New Zealand showing samples and sites inside (purple) and outside (green) of the putative refugial area occupied by eastern moa during the Last Glacial Maximum (purple shading). The accompanying network illustrates the relationships between the mitochondrial haplotypes. From: Verry et al. (2022).

The Story of the Moho and Takahē

After our stop in the Pleistocene, we jump further back in time. About four million years ago, a bird arrived in New Zealand which would later give rise to two flightless species: the Moho and the South Island Takahē. Fast forward to much more recent times, where both species faced dramatic declines following human arrival: first with Polynesian settlement between 1250 and 1300, and later with European colonization in the 18th century. One species went extinct, while the other managed to persist.

In contrast to the sustained human population pressure in the North Island that likely led to the extinction of moho, the reduced human pressure in the southern South Island apparently allowed takahē to persist as a small isolated population in the remote, mountainous Fiordland region. 

The human impact is clearly visible in the DNA of the South Island Takahē. A temporal comparison of mtDNA showed a marked loss of genetic diversity, coinciding with the human arrival about 750 years ago (and an additional decline across the Pleistocene-Holocene transition).

Temporal haplotype networks of mitochondrial DNA across three discrete time periods (based on subfossil bones, museum specimens/skins and contemporary samples) show a clear decline in genetic diversity for the South Island Takahē. Each circle corresponds to a distinct haplotype with the size proportional to its frequency. From: Verry et al. (2024).

A Molecular Time Machine

These studies show how ancient genomes allow scientists to peer into past populations, retrace their evolutionary journeys, and even uncover patterns that are invisible in the fossil record. Who needs a time machine when you have DNA?

References

Verry, A. J., Mitchell, K. J., & Rawlence, N. J. (2022). Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus). Biology Letters, 18(5), 20220013.

Verry, A. J., Mas‐Carrió, E., Gibb, G. C., Dutoit, L., Robertson, B. C., Waters, J. M., & Rawlence, N. J. (2024). Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand’s enigmatic takahē and moho. Molecular Ecology, 33(3), e17227.

Featured image: South Island Takahē (Porphyrio hochstetteri) © Bernard Spragg | Wikimedia Commons