Every individual kākāpō sequenced in latest recovery effort

New analysis of genomic sequencing for 169 individual kākāpō is the latest science salvo in decades of intensive efforts to stave off the bird’s extinction.

Director of Genomics Aotearoa and University of Otago Professor Peter Dearden describes the research into New Zealand’s critically endangered flightless and nocturnal parrot as “a Rolls Royce situation”. He says that’s “a remarkable thing, and a joy to behold”.

Dearden is co-author of the latest kākāpō research, published in Nature Ecology and Evolution, which analyses a dataset of 169 individual kākāpō genomes (sequenced for nearly every bird living at the time the data was collected) together with extensive information on the birds’ life histories collected by New Zealand’s Department of Conservation.

First author of the study, University of Otago researcher Joseph Guhlin, says for a “tiny species – gone down to 50 individuals and up to 252 – there’s a lot of cool evolutionary questions that can be answered [through the analysis], and  a lot of practical stuff to get more cute birds roaming the islands.” 

The paper focuses on findings with practical outcomes for conservation. 

Guhlin’s analysis compared variations between the 169 kākāpō individuals against the reference genome for the bird. He was able to connect genetic data to important survival traits for each bird, such as how many eggs a bird laid, or growth rates.

And with the help of artificial intelligence tools, he says, “we were able to see when certain variants aren’t passed down”.

The findings suggest earlier kākāpō conservation actions had largely been beneficial, illustrating that “active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential”.

For example, the decision to combine the kākāpō population on Stewart Island with one individual from Fiordland did help improve the genetic diversity of the population, Dearden says.

“We’ve shown that actually that contribution is beneficial to the population, the offspring of that kākāpō – whose name is Richard Henry – benefited the population in general and their offspring tend to lay more eggs and have faster growth rates,” he says.

When they started this work, the researchers thought the paper would be a complete catalogue of every indiviudal kākāpō. 

But Dearden says, in positive news “the last two seasons have been the best breeding seasons so far for kākāpō . There’s almost twice as many kākāpō now than when we did the study.”

“We’ve sequenced the genomes of all those chicks as well, and that data arrived in a big lump a couple of weeks ago,” he says.

The researchers hope their analysis can provide a kind of genetic guide for each chick, and potentially provide warning signs to conservation workers when things don’t line up.

Dearden gives an example in the case of growth rates. “Just from the genome sequence of the parents  – we know who the parents are, and we know the bird is on a particular island and being fed a particular diet, then we can predict the growth rate for it. And that means if it deviates from that growth rate, something’s wrong.”

They hope the analysis might also be useful in informing conservation decisions designed to maintain genetic diversity, such as which birds to use for artificial insemination, or to place on certain islands.