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Ancient DNA Survey Highlights Historical Biodiversity in New Zealand

NEW YORK (GenomeWeb) – A new genetic screen, encompassing thousands of pooled ancient bone samples, has provided insights into the past biodiversity present in New Zealand.

Researchers from Australia, New Zealand, and Denmark used a bulk, barcode sequencing-based method to screen more than three dozen subfossil assemblages containing thousands of bone fragments from sites going back 20,000 years, revealing DNA from more than 100 bird, fish, amphibian, reptile, and marine mammal species. The findings, reported online this week in the Proceedings of the National Academy of Sciences, provide a glimpse at rare species as well as extinct representatives from lineages that remain in the region.

"[T]his molecular audit of New Zealand's subfossil record not only contributes to our understanding of past biodiversity and precontact Maori subsistence practices but also provides a more nuanced snapshot of anthropogenic impacts on native fauna after first human arrival," senior author Michael Bunce, a molecular and life sciences researcher at Australia's Curtin University, and his colleagues wrote.

Prior studies suggest that New Zealand split off from a larger Gondwana supercontinent an estimated 55 million years ago, the team explained, remaining free from land mammals, including humans, for large stretches of its history. In the interim, the islands became home to a wide range of other animals, including flightless birds, such as the moa and kakapo.

"Over time, the ecological niches filled by mammals elsewhere were taken over by birds, giving rise to a variety of flightless avifauna found nowhere else in the world," the authors noted. "However, since the arrival of Polynesian settlers to the archipelago 750 years ago, the terrestrial avifauna has nearly halved, and at least 64 species of New Zealand's endemic birds and reptiles have become extinct, with new species added to the extinction list each year."

Using a sequencing-based screening approach called Bulk Bone Metabarcoding (BBM), the researchers sought out genetic clues to the country's past biodiversity, assessing DNA in 70 bone powder samples produced using 5,276 bone fragments dated at up to 20,000 years old. The bone samples came from museum collections and originated from 38 bone deposit sites — from the Pleistocene and Holocene, as well as just 200 years old — that were included in past archeological or paleontological studies.

When the team analyzed more than 1.8 million DNA sequence reads generated with this metabarcode assay method, it identified more than 650 operational taxonomic units, including taxa representing at least 54 bird species, 29 bony fish, and 21 mammals.

The latter group encompassed nine marine mammalian species, ranging from fur seals, sea lions, and elephant seals to dolphins and rare whale species. By following the trajectory of such marine mammal populations over time, the researchers attempted to retrace the use of seals and whales by the Maori people. A similar analysis allowed them to investigate historical fishing sources and technologies in the region.

The screen also led to DNA from extinct Leiopelma frog lineages that dwindled with declining habitat availability and the introduction of Pacific rats, the team reported. It also included DNA sequences from extinct flightless birds and kakapo haplotypes no longer found in New Zealand.

"Collectively, these findings highlight the impacts that human arrival had on biodiversity across New Zealand," the authors wrote, noting that "identification of moa and pinniped [seals] DNA throughout early Maori sites confirm that these species were hunted up until their extinction/extirpation in the 15th century." 

"In contrast, the absence from Maori middens of other extinct species that survived into the 20th century, such as the bush wren, kokako, and laughing owl, indicate that activities by European settlers were likely drivers of their decline," they added, while information on existing species helped to detect genetic diversity declines in animals with declining populations or habitat ranges.

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