Alpine forest genomics—advances in the research field and perspectives ahead

Abstract Key message Alpine or mountainous forest genomics research is rapidly moving from classic population genetic studies toward exploring population environmental adaptation to address climate vulnerabilities. For alpine conifers in particular, future progress in sustainable management relies heavily on overcoming the current bottleneck in the availability of genomic and experimental resources through targeted, interdisciplinary research efforts. Context Mountainous forests are among the most vulnerable ecosystems to climate change. Over the past two decades, rapid advances in high-throughput sequencing have transformed research on mountainous tree species, enabling a transition from marker-based population genetic studies to genome-wide analyses of demography and adaptation. Aims Here, we present a quantitative survey of how the field of mountainous or alpine forest genomics has evolved and provide future perspectives. Methods We conducted a bibliometric analysis of 662 research articles published between 2000 and 2024, focusing on seven of the most important high-elevation European conifer species. Topic modeling and co-occurrence network analyses were used to identify major research topics and their dynamics in time. Moreover, members of the Alpine Forest Genomics Network (AForGeN, IUFRO Working Party 2.04.11) were asked in a survey to indicate future priorities and challenges of the field. Results Our results show that publication activity has increased substantially after 2010 and that Picea abies (59%) was the most studied species. Topic modeling identified eight major research areas, and their temporal trends revealed a shift from genetic diversity and population structure studies towards environmental adaptation genomics. Co-occurrence analysis indicated two major clusters: population genetics and functional genomics research. Survey responses showed that there is an agreement that adaptation genomics will dominate the research of mountainous forests in the upcoming years, although the infrastructure, funding, and genomic resources remain major constraints to the development of this area of research. Conclusions Our findings demonstrate a clear shift of the research field towards adaptation genomics, yet progress is hindered by a lack of genomic resources for non-model species and a gap in functional validation. To inform climate-resilient management of mountainous forests, the field must move beyond association patterns towards identifying the underlying mechanisms, e.g., by integrating ecophysiological and epigenetic studies. Such interdisciplinary efforts are essential to develop robust and actionable conservation and management strategies.