How researchers have found a way to monitor the endangered kākāpō species through DNA found in soil.
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The kākāpō (Strigops habroptilus) is a flightless bird in the parrot family native to New Zealand. Their deep ‘boom’-like call is reminiscent of an owl as is their nocturnal nature. Kākāpōs are known for their cute appearance and bright green feathers, however, invasive predators such as polynesian rats don’t seem to care. Along with invasive mammalian predators such as rats – inbreeding, habitat fragmentation, and disease have placed the kākāpō high on the endangered list. Currently there are only 247 kākāpōs left alive with some residing in captivity at aviaries such as Whenua Hou (“Kākāpō | DOC”).
In the wild, endangered species such as the kākāpō require constant monitoring to ensure population health. Traditional methods used to monitor endangered species can require capturing the animals to fit them with trackers or taking blood samples. Not only does this put stress on the animals but it requires high cost and labor demands.
A team led by Lara Urban set out to address this issue by performing a study on the kākāpōs held in the Whenua Hou aviary mentioned above (Urban et al. 2023). Inspired by work where DNA from feathers and fecal matter was used to monitor endangered species (Ramón-Laca et al. 2018), they sought to do the same with DNA from environmental samples like soil and water.
Extracellular or environmental DNA also known as eDNA is a form of DNA – which if you do not know contains all the genetic information for an individual. eDNA is DNA extracted from environmental sources like water, soil, and even air (Bairoliya et al.) (Clare et al. 2021). It is a result of feces or tissue cells washing into the surrounding environment.
In practice, eDNA can be a difficult way to monitor individuals of a specific species. This is because eDNA samples contain a mixture of DNA from various organisms. Urban and her team address this with a metabarcoding approach. Metabarcoding is a technique that can identify multiple species in a mixed sample. Along with metabarcoding the researchers used a Bayesian inference approach to tell individuals apart within the same species. You do not need to understand the specifics of metabarcoding or Bayesian inference, but they both involve complex analysis and processing. These more complex methods beg the question – how accessible is this technology? For a trained conservationist the answer may be very, especially compared to previous methods.
The actual reading of the DNA is done with something known as nanopore sequencing. The DNA extracted from the eDNA sample is placed in a small nanopore machine that can plug into a laptop. It threads the DNA through a small sensor that reads the DNAs code. The DNA is typically read in small pieces, meaning it is not the full DNA found in the animal. Thus, a reference genome – a template of the complete kākāpō DNA sequence – is needed in order to match up the DNA pieces to each other. Once the pieces are matched up to create long enough DNA stretches, known as haplotypes, an individual can be identified as well as its genomic diversity – a fancy term for how one individual varies compared to others within its species.
Thanks to this technology eDNA now has the ability to tell conservationists the population fluctuation, species distribution, and individual genomic diversity of endangered species. These terms may sound complicated, but they all measure different aspects of an endangered species’ health. Previously, these metrics could not be retrieved from eDNA. Traditional methods required blood sampling or handling of the animal. Now critical information can be extracted from less than 1 gram of soil.
Urban and her team have now set forth a non-invasive, real-time method for tracking the health of endangered species. This is a huge step for conservationists, namely the New Zealand Department of Conservation, who are hoping to use these methods to track the range, health, and reproductive success of the remaining 247 kākāpōs. In addition to tracking already known individuals, conservationists are hoping to find any remaining, unidentified kākāpōs by analyzing soil samples throughout their wild habitats.
In addition to endangered species, Urban expresses potential to use this technology on rare and elusive species – how cool! Animals that may be hard to capture for sampling can now be analyzed through water or soil at locations they have previously been observed. One example of this application is the study of polar bears which are both endangered and elusive (Hellström et al. 2023).
Often times, advancements in genetic technology result in a complex ethical debate. In this case, however, I think only good things can be said about eDNA. It is perhaps too complex for the everyday person to use – and consequently abuse – but relatively straightforward for a trained conservationist. From a conservation standpoint, eDNA is more ethical for the animals being studied as they are not disturbed by the analysis.
A different question to be had is how “real-time” this technology actually is? While it is much faster and easier than traditional DNA analysis techniques there are still several steps involved in the approach. Among the steps are taking the actual sample, extracting the DNA in a lab, metabarcoding, nanopore sequencing (12 hours), and data processing. Altogether this does not seem very “real-time” to most. In order to truly claim the term, further technological advancements will need to take place.
Any limitations aside, eDNA sequencing is a promising step toward the conservation of endangered species like the kākāpō, and hopefully many more.
Sources
Bairoliya S., J. Koh Zhi Xiang, and B. Cao, Extracellular DNA in Environmental Samples: Occurrence, Extraction, Quantification, and Impact on Microbial Biodiversity Assessment. Appl. Environ. Microbiol. 88: e01845-21. https://doi.org/10.1128/aem.01845-21
Clare E. L., C. K. Economou, F. J. Bennett, C. E. Dyer, K. Adams, et al., 2021 Measuring biodiversity from DNA in the air. 2021.07.15.452392. 10.1016/j.cub.2021.11.064
Hellström M., E. Kruger, J. Näslund, M. Bisther, A. Edlund, et al., 2023 Capturing environmental DNA in snow tracks of polar bear, Eurasian lynx and snow leopard towards individual identification. Front. Conserv. Sci. 4. https://doi.org/10.3389/fcosc.2023.1250996
Kākāpō: New Zealand native land birds | Department of Conservation (DOC). https://www.doc.govt.nz/nature/native-animals/birds/birds-a-z/kakapo/
Ramón-Laca A., D. J. White, J. T. Weir, and H. A. Robertson, 2018 Extraction of DNA from captive-sourced feces and molted feathers provides a novel method for conservation management of New Zealand kiwi (Apteryx spp.). Ecol. Evol. 8: 3119–3130. https://doi.org/10.1002/ece3.3795
Urban L., A. K. Miller, D. Eason, D. Vercoe, M. Shaffer, et al., 2023 Non-invasive real-time genomic monitoring of the critically endangered kākāpō. eLife 12. https://doi.org/10.7554/eLife.84553.1
Written by: Susannah Armstrong, suarmstrong@davidson.edu
© Copyright 2022 Department of Biology , Davidson College, Davidson, NC 28036
This article was an interesting connection to our class discussion about genomics and conservation biology because it highlights how endangered species can be monitored using genomics methods. I think that there are really exciting applications of this work in terms of extending this approach to monitoring the health of other endangered species. I also agree with your point about the limitations of this method and how the amount of different steps required means the results aren’t necessarily a real-time reflection of the population being studied. It would be interesting to learn if there have been other methods considered to address this issue.
This article presents an interesting crossroad between genomic analysis and conservation studies. As more advancements are made in both the genomic and conservation funding/tech, I agree with you that only good can from it in regards to these types of studies, versus the frequent ethical conundrums that genomic advancements tend to lead to. I find this whole practice incredibly fascinating, the fact that they are able to more-or-less track these bird populations without putting additional survival stresses on the organisms seems like the best of both goals even if it lacks “real-time” data. I think the way you talked around and through this experimental process was both informative and easy to understand for a lay audience so much so I think if someone outside of our class read this they would also feel encouraged to look up the newest update on the cute little bird from your embedded image. Overall I really liked how you explained the paper, highlighted the limitations, but maintained a very positive and optimistic tone that these efforts will not be done in vain.