Interview with the authors: Applying genomic data in wildlife monitoring

Massive parallel sequencing has led to an explosion of sequence data in recent years. However, the methods used to obtain such data are usually high-cost and time-intensive, and often require high-quality samples. This creates limits as to whether and how well such data can be used by researchers working in applied conservation science. Here, we speak to Alina von Thaden about her recent study in Molecular Ecology Resources. Using European wildcats as a case study, Alina and co-authors present a relatively low-cost and time-efficient workflow for the development and optimisation of microfluidic SNP panels, which can be used to obtain SNP data from minimally invasive samples. Beyond outlining the workflow and its applications, they go so far as to estimate the costs of their pipeline, providing valuable practical information for conservation scientists. Read on for an in-depth view of this study.

Monitoring elusive European wildcats (Felis silvestris) is heavily reliant on noninvasively collected DNA samples. Photo credit: Annsophie Schmidt.

What led to your interest in this topic / what was the motivation for this study? 

We are mainly working on genetic monitoring of large carnivores and most of our research is based on noninvasively collected wildlife samples such as hairs, faeces and saliva traces. The field demands for very fast and reliable genetic analyses of samples with degraded DNA. And since funding is generally sparse in applied conservation, our methods need to be cost-effective and suitable for high-throughput approaches.

Genomic tools, on the other hand, usually involve large amounts of data, complex bioinformatic pipelines and typically rely on samples with high-quality DNA. We have been looking into ways to combine the advantages of genomics with the challenges of conservation monitoring. For some years now, we have been working with microfluidic arrays combined with reduced SNP panels and wanted to share our experiences with other labs interested in applying them.

What difficulties did you run into along the way? 

Setting-up and optimizing methodological resources comes along with several challenges – but there is a lot to learn! Most important to me was to remain skeptical about the results and to constantly validate them through analyzing the data from several perspectives and with different software. The validation of the technology also took a lot of extra lab hours, but we are confident that the workflow and guidelines that we present now will save others a lot of hands-on time and costs when optimizing SNP panels for degraded samples.

What is the biggest or most surprising finding from this study? 

First of all, after years of developing the framework, we applied it to a new SNP panel designed for dog-wolf hybridization assessment (to be published) and found that the lab work for generating a new ready-to-use marker panel took us only a few weeks. To see the approach being proved effective was great and encouraged us to share it with the community.

Secondly, a large proportion of noninvasively collected samples could be run without or with only very few genotyping errors as compared to more traditional microsatellite-based genotyping (see also von Thaden et al. 2017). This has direct implications for genotyping costs and thus promotes the broader establishment of a genomic technology in applied conservation.

Alina von Thaden collecting reference samples of European wildcat (Felis silvestris) for testing a newly developed SNP panel. Photo credit: Annsophie Schmidt.

Moving forward, what are the next steps for this research? 

One of our next steps is to apply the technology to historical samples from museum collections. Additionally, we are going to implement the SNP panel from our current paper in routine genetic monitoring of European wildcats in Germany.

We currently develop other reduced SNP panels for a variety of endangered species in our lab, such as dormice and European bison. Besides neutral variation, we also aim to integrate functional markers, such as SNPs associated with disease susceptibility.

Further, we will test alternative platforms that will allow generating larger SNP sets for degraded samples. Ultimately, our long-term goal is the effective implementation of an “applied genomic wildlife monitoring” approach.

What would your message be for students about to start their first research projects in this topic? 

Get in contact with other groups working in this area! Sharing ideas and experience really helps to shape your project and refine the aims of your research. Most people are very cooperative and happy to contribute or answer questions.

What have you learned about science over the course of this project? 

Perseverance and tenacity. When exploring new directions the research journey may well become bumpy and lead you somewhere else than you initially expected. But it’s worth it – keep your goal in mind and be ready to rethink your strategy.

Describe the significance of this research for the general scientific community in one sentence.

Bridging the gap between genomics and applied conservation is a key prerequisite for effective wildlife management, especially in the light of rapid biodiversity declines.

Describe the significance of this research for your scientific community in one sentence.

We demonstrate how reduced SNP panels can be efficiently developed and optimized for genotyping based on degraded wildlife samples.

References

von Thaden, A., Cocchiararo, B., Jarausch, A., Jüngling, H., Karamanlidis, A. A., Tiesmeyer, A. … Muñoz-Fuentes, V. (2017). Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays. Scientific Reports, 7, 83. https://doi.org/10.1038/s41598-017-10647-w

Full paper

von Thaden, A., Nowak, C., Tiesmeyer, A., Reiners, T. E., Alves, P. C., Lyons, L. A., … & Hegyeli, Z. (2020). Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism (SNP) panels. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13136

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Interview with the authors: glacial refugia and the dispersal of terrestrial invertebrates

Antarctica is an extreme and isolated environment that supports a variety of species. However, we know little about how terrestrial species survive in these kinds of conditions. In a recent paper in Molecular Ecology, McGaughran and colleagues investigated a widespread group of terrestrial invertebrates to understand how species have persisted in this harsh environment. These researchers found that there were many local clusters of individuals with substantially more long-distance dispersal events than were previously identified. These long-distance dispersers were likely aided by wind, providing an interesting example of the link between environmental conditions and population stability. For more information, please see the full article and the interview with McGaughran, lead author of the study, below. 

Antarctic Peninsula taken near the tip. Photo created by Dr. Ceridwen Fraser.

What led to your interest in this topic / what was the motivation for this study? 
During my PhD, I researched genetic and physiological diversity of Antarctic terrestrial invertebrates, spending a collective ~6 months on the ice.  I then stepped away from Antarctic research for several years, completing postdocs in Germany and Australia, but I never forgot my time in Antarctica or my love for its unique environment.  Thus, I’ve maintained collaborative links that have allowed me to continue to contribute to Antarctic research.  In this study, we wanted to see whether genomic data would give us greater insight to the evolutionary history of invertebrates along the Antarctic Peninsula than had been gained with single-gene analysis in the past.  

What difficulties did you run into along the way? 
Getting workable quantities of DNA from tiny (~1 mm) springtails to use in genomic applications is difficult.  In fact, for this study, we tried to extract DNA from several Antarctic springtail species, but were only successful in our attempts with Cryptopygus antarcticus antarcticus.  Low DNA concentrations can also mean that the genomic data we end up with for analysis is patchy.  These aspects provide some challenges, but the methodologies underlying library preparation and sequencing are continually improving and we are excited about the potential of applying genomic methodologies to more Antarctic taxa in the future.

What is the biggest or most surprising finding from this study? 
Using genome-wide data, we were able to find evidence for a greater frequency of dispersal events than had been previously shown with single-gene data.  This was particularly surprising because dispersal for Antarctic invertebrates is hard.  These animals live under the rocks in moist ice-free areas.  As soon as they leave the relative safety of the soil column, they are exposed to freezing and desiccating conditions.  Thus, though we have some evidence to suggest that springtails can survive for short periods in humid air columns or floating on water, our expectation is that such events would be rare.  Finding genetic evidence that suggested several instances of successful dispersal over extremely long geographic distances was therefore surprising.

Moving forward, what are the next steps for this research? 
Much of the Antarctic literature focused toward understanding evolutionary and biogeographic questions has been based on single-gene analyses because genomic approaches are still relatively new.  This previous work has been informative about the fact that many Antarctic terrestrial species have survived glaciation in refugia, but there is much that remains to be discovered.  Antarctica is a kind of barometer for the rest of the world and it is important that we understand how species there have responded to environmental change in the past and how they may do so in the future.  Thus, key to extending this research will be to bring genomic approaches to bear on other populations and species in Antarctica.  This will help us to gain an understanding of how isolated Antarctica really is, and how its endemic species will likely respond to future environmental changes.

What would your message be for students about to start their first research projects in this topic? 
In this genomic and associated bioinformatic era, learning the skills of a well-rounded biologist who has a breadth of understanding that spans the field, the laboratory, and the computer, can be daunting.  As you develop or use novel techniques in Molecular Ecology, my message would be to stick with it through the hard stuff.  It is such an exciting time to be an evolutionary biologist and, though it can involve some really tough moments, the revelations we can achieve about how the world works are key.  Alongside this, I would suggest that collaboration is now more important than ever – don’t feel like you have to reinvent the wheel or be an expert on every single aspect of your research.  Instead, develop your own niche and share in the expertise of those around you to do the best science together.

What have you learned about science over the course of this project? 
When I first started doing research, there was no such thing as genomics or next generation sequencing and we simply didn’t have the means to gain genome-wide data.  In recent years, the face of evolutionary biology has changed due to the revolution in sequencing technology and bioinformatics.  As exemplified by this project, I’ve learned that genomic data can provide new and more nuanced insights into our biological questions of interest.  And, though it can be hard at times to work in such a swift-moving area of research, it is ultimately very rewarding.

Describe the significance of this research for the general scientific community in one sentence.
The environment, especially wind, plays an important role in structuring patterns of genetic diversity among Antarctic populations – thus future climatic changes are likely to have a significant impact on the distribution and diversity of these populations.  

Describe the significance of this research for your scientific community in one sentence.
Bringing genomic data to bear on long-standing evolutionary questions in Antarctica is a worthwhile and fruitful endeavour that will ultimately produce greater insights into understanding and protecting Antarctic taxa.

Dry Valleys taken in the Antarctic Dry Valleys. Photo created by Dr. Angela McGaughran.

McGaughran A, Terauds A, Convey P, Fraser CI. 2019. Genome‐wide SNP data reveal improved evidence for Antarctic glacial refugia and dispersal of terrestrial invertebrates. Molecular Ecology. 28:4941-4957. https://doi.org/10.1111/mec.15269.