Analysis of entire genomes from New Zealand’s critically endangered, flightless parrots found they carry exceptionally few harmful genetic mutations despite 10,000 years of inbreeding. How did they manage this?
The first ever genomic analysis of the critically endangered kākāpō, Strigops habroptilus, has revealed the flightless parrots carry surprisingly few harmful genetic mutations, despite the fact that the species has inbred for many centuries. This is contrary to what is typically seen for inbreeding.
Basically, when there are very few breeding adults remaining in a small population, one of two genetic outcomes will occur: either harmful mutations accumulate randomly throughout the genome or, alternatively, harmful mutations may decrease due to genetic purging. Of these two scenarios, the accumulation of harmful mutations is the most likely scenario.
Unless you are a kākāpō, apparently.
In 1995, the kākāpō population reached its nadir when just 51 of the charismatic moss-green parrots were still alive in the world: 50 were sequestered on tiny Stewart Island, located south of New Zealand’s South Island, and a single male, named Richard Henry, was the last living individual on New Zealand’s mainland. Due to the diminutive size of this remnant population, scientists predicted that kākāpō were severely inbred, and they also predicted that this situation would probably impair conservation efforts to save this species. Inbreeding is typically is the recipe for a “mutational meltdown”, a situation that rapidly leads to extinction due to an accumulation of excess of deleterious mutations.
Mutations are random changes to the genetic code of living beings. Like typographical errors in text, changes in DNA are accidents and, because plants and animals are so supremely well adapted to their environment, almost all mutations are harmful. In large populations, mutations have a much smaller effect on the overall health of the population and further, natural selection often removes harmful mutations by eliminating the individuals carrying them. Unlike in large populations, any one individual in a small population can have an outsized impact on the genetic health of the entire species. Thus, harmful mutations spread and accumulate, causing the population to decline further and accelerate towards extinction.
Considering the high levels of inbreeding in the few remaining kākāpō, Nicolas Dussex, a researcher at the Center for Palaeogenetics, and at Stockholm University, wondered if a growing accumulation of random deleterious mutations was at least one of the problems bedevilling the kākāpō recovery effort, which is seeing an extremely slow response to intensive conservation efforts to save these iconic parrots. They also wanted to use genomics to help choose appropriate mates for each bird. To address these issues, Dr Dussex and some of his colleagues assembled a huge international team of scientists from Sweden and New Zealand. The team obtained samples from a total of 49 individual kākāpō: they collected a little blood from 35 birds living on Stewart Island and toe pad scrapings from 14 museum specimens that were part of the historic (but now extinct) mainland population.
Using these samples, the research team generated high quality chromosome-level genome assemblies from the 36 individual kākāpō (Richard Henry and 35 Stewart Island birds) that survived the genetic bottleneck at its most severe phase in the 1990s as well as 13 genomes from the museum specimens (each approximately 130 years old) that originated from the extinct mainland population.
The team conducted the first-ever detailed analysis of these genomes and identified genetic distinctions between the extinct mainland and extant Stewart Island populations (Figure 1B). They also calculated the total genetic burden from accumulated mutations for both the living and the historic kākāpō populations. This genetic burden, more formally known as the ‘mutational load’, exists as a delicate balance between natural selection that removes deleterious mutations from the population and the random accidental generation of more deleterious mutations.
Contrary to popular belief that kākāpō were translocated to Stewart Island by either Maōri settlers or European colonists around 500 years ago, Dr Dussex and his collaborators found that the divergence between the mainland and the Stewart Island populations dates back to the end of the last glacial period. This coincides with the isolation of Stewart Island from mainland New Zealand as sea levels rose at the end of the Pleistocene some 12,000 years ago. Thus, the Stewart Island population is a distinct lineage that has been isolated from the mainland kākāpō for as long as 1,000 generations.
This long period of isolation, combined with the severe decline of the Stewart Island population during the past 150 years could have further decreased the genetic diversity of the remaining kākāpō. Dr Dussex and his collaborators investigated this possibility and found that large portions of Stewart Island kākāpō genomes were identical due to recent mating between closely related individuals, probably during the past ten generations. Dr Dussex and his collaborators then compared the genomes from the mainland kākāpō and the Stewart Island kākāpō, and were surprised to find that the Stewart Island birds have around half as many harmful mutations as those that lived on the mainland more than a hundred years ago.
“Even though the kākāpō is one of the most inbred and endangered bird species in the world, it has many fewer harmful mutations than expected,” Dr Dussex said in email.
But how did a highly inbred species like the Stewart Island kākāpō end up with so few harmful mutations?
“Our data shows that the surviving population on Stewart Island has been isolated for approximately 10,000 years and that during this time, harmful mutations have been removed by natural selection in a process called ‘purging’ and that inbreeding may have facilitated it.”
This is good news for kākāpō and other severely endangered species that may have been inbred for hundreds of generations or longer. It is possible that an endangered species may not suffer the harmful effects of inbreeding. Indeed, whether a population experiences either genetic ‘meltdown’ or genetic purging depends on its situation. In the case of kākāpō, genetic purging was the result of a small long-term population size, followed by an even more recent, and severe, population decline.
Is it possible that kākāpō might recover from this decline?
“While the species is still critically endangered, this result is encouraging as it shows that a large number of genetic defects have been lost over time and that high inbreeding alone may not necessarily mean that the species is doomed to extinction,” Dr Dussex said.
“It thus gives us some hope for the long-term survival of the kākāpō as well as other species with a similar population history.”
But are kākāpō special in this respect? Or might this situation apply to other extremely inbred animals too? This is a possibility, but this is the next question that Dr Dussex is looking to answer.
Nicolas Dussex, Tom van der Valk, Hernán E. Morales, Christopher W. Wheat, David Díez-del-Molino, Johanna von Seth, Yasmin Foster, Verena E. Kutschera, Katerina Guschanski, Arang Rhie, Adam M. Phillippy, Jonas Korlach, Kerstin Howe, William Chow, Sarah Pelan, Joanna D. Mendes Damas, Harris A. Lewin, Alex R. Hastie, Giulio Formenti, Olivier Fedrigo, Joseph Guhlin, Thomas W.R. Harrop, Marissa F. Le Lec, Peter K. Dearden, Leanne Haggerty, Fergal J. Martin, Vamsi Kodali, Françoise Thibaud-Nissen, David Iorns, Michael Knapp, Neil J. Gemmell, Fiona Robertson, Ron Moorhouse, Andrew Digby, Daryl Eason, Deidre Vercoe, Jason Howard, Erich D. Jarvis, Bruce C. Robertson and Love Dalén (2021). Population genomics analyses of the critically endangered kākāpō, Cell Genomics, published online on 8 September 2021 ahead of print | doi:10.1016/j.xgen.2021.100002
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