Researchers discuss the significance of this new genome and the need for collaborations beyond academia to protect the future of one of Europe’s most iconic mountain dwellers.
The first high-quality reference genome sequence for the iconic chamois (Rupicapra rupicapra) was produced as part of the Biodiversity Genomics Europe Project and is now openly available. We spoke with Profs. Elena Bužan and Boštjan Pokorny, Slovenian researchers whose work supports the science-based management of the chamois and other native species. They share insights on the Alpine chamois, its significance to local communities, the many applications of a new reference genome, and the importance of collaborating with stakeholders beyond academia to ensure the effective conservation of this and other species. Watch the video for highlights of this conversation and read the full interview below:
Prof. Elena Bužan is a molecular ecologist at the University of Primorska. She applies evolutionary genetics to biogeography and conservation biology, with main focus on the impact of habitat fragmentation and degradation on genetic population structure of small mammals and ungulates such as the chamois.
Prof. Boštjan Pokorny is dean of the Faculty of Environmental Protection, Velenje, Slovenia, chair of the scientific council of the Hunter’s Association of Slovenia and a senior researcher at the Slovenian Forestry Institute.
Could you introduce the northern chamois and briefly describe the main conservation challenges faced by this species?
Elena Bužan: The northern chamois is one of the two chamois species found in Europe (the second one is southern chamois) and it is the most abundant ungulate species in Europe and the near East. According to recent taxonomic studies, the northern chamois is divided into seven subspecies, some of which are quite threatened due to factors such as population isolation, poaching, overhunting, human disturbance in the environment, habitat degradation and loss and also climate change happening now in mountainous regions. Despite all these issues, the Alpine chamois - the subspecies for which we just sequenced the reference genome - is categorized as “least concern” in the IUCN’s Red List of Threatened species, so is not considered to be of a very high conservation concern.
Boštjan Pokorny: The Alpine chamois is an iconic inhabitant of Alpine areas in Europe, including Slovenia, and this is one of the reasons why we nominated this subspecies to have its genome sequenced. In Slovenia, the whole management and conservation program for the species is based on sustainable management made by hunters. As Elena said, even though the northern chamois is still considered as “least concern” by the IUCN, in the Alpine area this subspecies have recently experienced several threads that lead to decline of local subpopulations - particularly in high mountain areas. There are several reasons behind this decline; very important are climatic changes that have affected and will continue to affect the Alpine chamois. Scientists observed very clearly that there has been a switch in the patterns of vegetation growth in the alpine high mountain areas. Due to the rise in temperatures, the vegetation period - the growing season for vegetation - is now starting earlier, while the reproduction period (mating season) for the chamois remains the same or is even delayed towards the end of the year. This leads to a difficult situation for chamois and other wildlife: before, the main breeding season was in sync with the peak of vegetation availability (and quality), but now this timing has been disrupted. Indeed, we can see a discrepancy between the moment when the best food resources are available and the moment when the animals are having their offspring. This is of course very negative for the species and the effect is really dramatic in some areas. Scientists in Europe have observed this effect very clearly both considering the decrease of the animal’s body mass - which is essential for having higher reproductive potential - as well as the lower number and winter survival of offspring.
In summary, even if the (sub)species is abundant and classified as “least concern” it still experiences several threats to its conservation. Another issue are the interspecific interactions - meaning interactions with other species. The red deer is an example: this species is going up into the mountain regions coming in very close vicinity to chamois. These new interactions have direct and indirect effects on the chamois since the two species now compete for the same food and other resources. I believe the main conservation threads to the northern chamois are climatic change and the introduction of competition with other ungulates (red deer) coming into the Alps, but also the direct effect of people (mainly due to disturbance) should not be neglected.
How will the newly sequenced alpine chamois reference genome help address these conservation challenges?
Elena: First of all, I would like to say that the whole scientific community working on chamois genetics will greatly benefit from the reference genome. Having this kind of standard resource and harmonization in downstream analyses will improve our ability to compare data across different labs - something that has been very challenging until now when using various molecular techniques and approaches. With the reference genome, we now have the possibility to move forward, for example, with whole-genome sequencing for various populations, which allows for better data comparisons among scientists conducting genomic studies across the chamois’ distribution range. An annotated reference genome will provide numerous opportunities, including studying adaptation to future climate change, estimating effective population sizes, and possible hybridisation events.
Having these tools is crucial for developing a comprehensive and holistic approach to genetic studies of the species across Europe. It is important to understand what is happening in populations across different regions, including the Pyrinenian and Apennine Peninsula, the Alps, the Balkan region, the Caucasus, and the Carpathians. Now is the right time to unite scientists working on chamois genetics to conduct truly comprehensive studies that will improve future research, management, and even conservation efforts. This is particularly relevant because some chamois subspecies are protected under the Habitats Directive, meaning they require specific conservation measures. A well-developed reference genome will help ensure that management and conservation strategies are based on the best possible scientific data.
Boštjan: Exactly, genetic analysis provides crucial information, such as estimating population abundance. In high-altitude areas, it is possible to count individuals, but this becomes much more challenging in forested regions where chamois are also present. In such cases, modern techniques like genetic analysis become essential, creating a win-win situation for both conservation and management.
Another application of the reference genome relates to potential reintroduction of the species. In the Southeastern Balkans, for example, there is potential for the reintroduction of the species in some mountain areas where it once existed but is no longer present. From this perspective, the new reference genome and comprehensive population data will be crucial for selecting the right populations for translocation. It may even be necessary to mix individuals from different populations to achieve the best possible outcome from the genetic viewpoint. While this is not currently a priority in our region, it is definitely essential for Southeastern Europe. As far as I know, this is also one of the expected outcomes of a case study within the BGE Project.
Genomic projects are often highly collaborative and involve a lot of people. Is this also the case in this work with the chamois?
Elena: Yes, it’s very important to realize that as scientists working with genomics we are always missing the perspective from the field. Even if collaborating with ecologists, it’s not enough, we always need more data from people who are in the field in direct contact with the species. For this reason it was really important for us to establish collaborations with hunters and local communities - they give us feedback about what is really happening in the field which enables us to react and investigate the changes using scientific methods. We do have quite a lot of experience working in this collaborative way. There are many ongoing projects in my research group that started because of questions or concerns that local hunters had and so they decided to approach us.
Boštjan: In the case of the Alpine chamois, we were asked both by the Slovenian Hunters Association as well as the Triglav National Park to develop scientific based backgrounds for developing monitoring and management programmes for the species. And a very important part of this research to improve species management includes using genomic data to answer several key questions, such as abundance estimates, evaluating species resilience to factors like parasites etc. It is really important that the end-users - doesn't matter if they are conservationists or members from the hunter’s association - really recognize the potential of science and that we help by providing some directions on how to improve the species management.
Elena: Especially because these stakeholders are increasingly open to using genetic information. It’s also a great moment for collaboration, as the cost of generating genetic data - once considered too expensive - has significantly decreased. It's encouraging to see that even end-users can now afford to finance genetic analyses, which will help raise awareness of how valuable genetic data can be. This information is essential for estimating genetic diversity, improving population management, assessing adaptive potential, and determining effective population size. In many cases, we still lack a clear understanding of population sizes and genetic health, both of which are crucial for long-term adaptation and conservation efforts.
Can you tell us a bit more about the situation in Slovenia? How was the start of this productive collaboration between academic scientists and other sectors interested in chamois conservation?
Elena: I can say that this collaboration is very connected to the first interest from the Triglav National Park, which is our largest national park. About ten years ago, we started collaborating with them, and at that time, we had already published the first genetic study, which was based on microsatellites. Over time, this collaboration expanded, including cooperation with hunters as well.
Boštjan: Basically, as Elena mentioned, the first study was published based on the interest of the Triglav National Park, and afterwards people working in wildlife management - in this specific case, chamois management - recognized the potential of genetics. The scientific community in Slovenia, working on wildlife, is very closely connected with the Hunters Association. For example, the Hunters Association of Slovenia established a Scientific council more than a decade ago - this is a unique situation in Europe. This council consists of nearly all experts working on wildlife monitoring, management, and research, including Elena and myself. Importantly, there are several members, like Elena, who are not hunters, which helps build trust and facilitate communication. In most European countries, researchers will simply ask hunters for samples, but they don’t always respect their knowledge, expertise, or the realities of their work. Without mutual trust between both communities (hunters and scientists), collaboration is impossible. We would like to introduce this approach across Europe, and many countries are already adopting it because the scientific community recognizes the value of such collaboration.
But if we focus solely on the chamois, it holds both an iconic and symbolic value for hunters. This species is highly recognized and valuable. It is even featured in the logo of the Hunters Association, not only in Slovenia but in several other regions. Historically, reaching the high-altitude areas where chamois live was challenging, making both hunting and managing the species difficult. Additionally, chamois do not have negative impacts on other sectors of society, such as landowners, particularly in mountain regions. From this perspective, it is truly a symbolic species, and hunters deeply appreciate and value it. When hunters notice issues in the field, such as a declining population trend of chamois, it raises serious concerns. For example, if the wild boar population were to decrease, hunters likely wouldn’t react strongly or would nowadays even do all the best to control the population. However, for chamois, a population decline is alarming. In response, population managers turn to scientists, relying on our expertise to improve management strategies.
Can you expand a bit on the role of the hunting association and other non-academic actors in the research for chamois conservation? Do they help you collect the samples or other data?
Boštjan: While sample and data collection represents one aspect of citizen science, we believe it is crucial not to limit our understanding of citizen science to just that role. Of course, the easiest approach is to ask for help with data collection, observations, and similar contributions. However, in many citizen science studies, we fail to use the full potential of citizen scientists, particularly their personal knowledge. When it comes to field observations, understanding general ecology, or interpreting animal behavior, citizen scientists - especially those with direct experience - can sometimes have knowledge comparable to that of scientists working in offices or laboratories. This makes their involvement not just beneficial but essential. The real challenge and opportunity lie in engaging citizen scientists not just as data collectors but as active contributors who help shape research questions and guide studies in the right direction.
For example, in chamois research, the knowledge held by hunting associations across the Alpine region is invaluable. Their expertise can help define key research problems, focus on the most relevant questions, and even aid in interpreting study outcomes. While citizen scientists may not always grasp the complex genetic results generated in a laboratory, they can certainly understand their practical implications. There is also an important distinction between different types of citizen scientists. The general public, for example, may contribute observations and data through apps, but they may lack the deep expertise needed to interpret broader ecological patterns. In contrast, groups such as hunters and fishermen are unique in that they not only engage with nature but also possess in-depth knowledge and experience. This is why including citizen scientists, especially those with specialized expertise, is so crucial for projects like this.
Elena: I would say that local and traditional knowledge, which can be held by specific groups such as hunters, fishermen, beekeepers, and others, is invaluable. Additionally, the knowledge possessed by local communities is especially important, particularly in alpine areas where long-standing traditions and histories exist. These communities can provide a lot of information about species - knowledge that we could never acquire solely through laboratory work or a few years of field observations. Their understanding is built on decades of observations, passed down from generation to generation, as they live as an integral part of these natural habitats.
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Interview and editing by Luísa Marins
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