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Analysis of Kiwi Genome Provides Clues to Nocturnal Adaptation

NEW YORK (GenomeWeb) – In Genome Biology, an international team of researchers presented their findings from a genome sequencing study of the North Island brown kiwi (Apteryx mantelli), a flightless bird species native to New Zealand.

The kiwi genome is one of the largest bird genomes sequenced to date. Researchers studying the bird identified evolutionary changes in its genome that may help explain the bird's unique nocturnal adaptation — a trait shared by fewer than three percent of all bird species, they noted.

For their study, the researchers, led by Diana Le Duc, from the University of Leipzig and the Max Planck Institute for Evolutionary Anthropology, Germany, sequenced the genomes of two North Island brown kiwis and compared them to that of the chicken and zebra finch. They found that nearly 92 percent of the zebra finch sequences that are syntenic-chain-alignable to the chicken showed conserved synteny in the kiwi, which suggested the kiwi genome assembly includes the majority of conserved regions between birds.

In addition, the researchers looked at 16 species of birds, mammals, and reptiles that share characteristics of the kiwi and fall within the same phylogenetic tree. An analysis of gene family functions that showed expansion in kiwi identified enrichment in categories such as signal transduction, calcium homeostasis, and motor activity. Investigators also delved into branch-specific selection to identify genes and functional pathways that they believed could underlie kiwi-specific adaptation.

The researchers found that the kiwi evolved certain unique traits absent in other species, including low metabolic rate, highly developed sense of smell, and enormous eggs relative to body size.

They also observed a loss of function in OPN1SW, the gene responsible for blue color vision, and OPN1MW, the gene responsible for green color vision, which is indicative of adaptation to nocturnality. A more diverse set of olfactory receptor genes, which are responsible for sensitivity to smell, were also assumed to indicate an adaptation to a nocturnal lifestyle, they said.

"We've seen for the first time that kiwi lack color vision, and that their olfactory receptors can probably detect a larger range of odors, which may be essential for their night-time foraging," Le Duc said in a statement. "These adaptations seem to have happened around 35 million years ago, soon after their arrival in New Zealand, probably as a consequence of their nocturnal lifestyle."

In 2014, researchers from Australia and New Zealand reported in Sciencethat the kiwi was in fact a sister species to the extinct elephant bird, a large member of the ratite family — bird species with flat breastbones that includes ostriches and emus. Their research established that flightless birds evolved much later in some ratite species than was previously understood. The kiwi broke off from the elephant bird line approximately 50 million years ago and didn't become flightless until after the kiwi's ancestors arrived in New Zealand millions of years later, they reported.

The German research team estimates that these changes occurred 30-39 million years ago, which means the kiwi adopted its nocturnal behavior shortly after its ancestor's arrival in New Zealand. Moas, now extinct birds from the ratite family, already lived in New Zealand when the kiwi's ancestors arrived. It's thought that moas, one species of which reached three meters in height, monopolized food sources during the day, which forced the smaller kiwis to adopt an alternative nocturnal lifestyle.

While the research team has unraveled some of the mysteries of kiwi’s nocturnal adaptation, they hope for more research in this field to fill in the blanks. Comparative analyses with other diurnal birds in the Palaeognathae clade, which include ostriches, emus, and cassowary, and additional nocturnal bird groups alongside their diurnal sister species will help make the evolution of adaptation in species clearer. They believe that this will greatly expand the information scientists have about genomic imprints of adaptation to a nocturnal lifestyle.

They also hope that more information about ratite species will help with protecting these unique species for the future.

"Despite conservation efforts, North Island brown kiwi are still at high risk of extinction," said Le Duc. "We made a first estimate of the diversity of the kiwi genome by comparing the sequence of two individuals, and it appears to be as low as that of inbred birds. This is an important indication of the level of the threat, and we expect further insights from the genome to help in developing conservation management strategies."