Alpine Forest Genomics Shifts From Population Genetics to Climate Adaptation

Mountain forests are among the ecosystems most exposed to climate change, and the science that studies their trees is changing just as fast. A new perspective article in Annals of Forest Science maps, for the first time, how the field of alpine forest genomics has evolved over a quarter century and where it is heading. The analysis, based on a systematic bibliometric survey of 662 research articles published between 2000 and 2024, shows a discipline in mid-transition: classic population genetic studies of genetic diversity and structure are giving way to genome-wide investigations of how high-elevation conifers adapt to their environment. The authors conclude that this shift is real and accelerating, but that it is being held back by a persistent shortage of genomic and experimental resources for the very species that matter most in mountain landscapes.

The study was carried out by researchers affiliated with the Alpine Forest Genomics Network, known as AForGeN, which operates as IUFRO Working Party 2.04.11. The network was founded in 2012 by researchers led by David Neale and held its eleventh meeting in Todtmoos in the German Black Forest in June 2026. To chart the field’s trajectory, the team searched the Web of Science database in January 2025 for publications from 2000 to 2024 that mentioned seven of the most important high-elevation European conifer species together with genetic or genomic terms. After manual filtering removed papers that did not directly study these trees, 662 of an initial 869 publications remained for analysis.

The publication record tells a story of steady growth. Annual output declined between 2002 and 2006, peaked around 2008 with 25 publications, and then climbed from 16 papers in 2009 to 50 in 2019. Since AForGeN’s foundation in 2012, publications involving network members have accounted for between 15 and 31 percent of the overall output in the field. One species towers over the rest: Norway spruce was the subject of 388 publications, or 59 percent of the total, followed by silver fir with 121 papers (18 percent) and European larch with 61 (9 percent). The authors attribute this dominance largely to economic importance rather than ecological priority, noting that less commercially valuable species such as Swiss stone pine and dwarf mountain pine remain underrepresented in genomic research despite their ecological significance in mountain ecosystems.

To identify what researchers were actually studying, the team went beyond simple keyword counts, which suffer from inconsistent terminology. Instead they applied topic modeling, a computational technique that clusters the vocabulary of titles, abstracts and author keywords into coherent themes. Using pairs of words weighted by how specifically they occur across the corpus, the researchers built topic models at two resolutions. An eight-topic model captured broad research categories: genetic diversity, quantitative genetics, seed orchards, genetic structure, climate response, wood properties, environmental adaptation and genome structure. A finer seventeen-topic model split these into narrower themes including breeding, gene expression, disease resistance, dendroecology and gene flow. The temporal trends were unambiguous. While publications on quantitative genetics and genetic structure dominated between 2000 and 2010, work on climate responses and environmental adaptation became markedly more frequent in recent years.

A co-occurrence network analysis, which maps how often topics appear together in the same papers, revealed that the field is organized into two distinct scientific clusters. One, described as population genetics, links genetic structure, genetic diversity, seed orchards, climate response and quantitative genetics. The other, corresponding to functional genomics, connects environmental adaptation, genome structure and wood properties. Across the full 25-year period, genetic structure was the most prevalent topic, appearing in 51 percent of publications, with environmental adaptation close behind at 45 percent. In the finer seventeen-topic network, genetic differentiation (32 percent) and genetic trait variation (26 percent) led the count. One detail caught the authors’ attention: genetic trait variation showed only limited association with breeding, suggesting that research on trait variation in alpine conifers remains focused on evolutionary ecology and natural populations, with few direct links to applied breeding programs.

The most cited papers reinforced Norway spruce’s role as the field’s model species. Thirteen of the eighteen most cited publications, all exceeding 100 citations, focused on P. abies. The standout was the study describing the nuclear reference genome of Norway spruce, published in 2013, which was the first conifer reference genome assembly ever published. The authors argue that this pattern reflects a well-known dynamic in model organism research: species with well-characterized genomic resources attract further projects and funding, which in turn generate new results, creating a self-reinforcing loop that leaves non-model species behind.

To look forward, the team surveyed the 93 members of AForGeN in December 2024 with open-ended questions about future priorities and challenges. Twenty-five members responded, a 27 percent response rate. The result was striking: 92 percent of respondents named adaptation genomics, or a closely related keyword, as a primary research topic for the coming years. After that came the establishment of genomic resources, the study of elevational and range shifts, and assisted migration and gene flow. When asked what they would personally study if there were no constraints, members again prioritized adaptation genomics, followed by more experimental work, genomic resources, biotic interactions and structural variants in the genome. Interestingly, some topics members expected to become important, such as assisted migration and range shifts, were almost never chosen for their own research, while topics like reproduction, hybridization and phenotypic variation interested them personally but were not seen as field-wide priorities.

The survey also laid bare the field’s bottlenecks. Financial, genomic and experimental resources were named as the main constraints on planned research, followed by missing know-how, including on tree biology, and sampling difficulties posed by rugged mountain terrain. Respondents noted that data and general knowledge about environments, phenotypes and gene functions are also lacking. The authors explain that the scarcity of genomic resources stems largely from the sheer size and repetitiveness of conifer genomes, which has led to missing or highly fragmented reference assemblies. Even where good references exist, whole-genome re-sequencing of many individuals remains expensive for species with huge genomes, which is why approaches such as reduced-representation sequencing, low-coverage or pooled sequencing, and SNP panels are still widely used, most of which themselves benefit from high-quality reference assemblies.

Help may be on the way. The authors point to recent advances in long-read sequencing, whose falling costs are expected to boost reference genome assembly for conifers. AForGeN is currently collaborating on an improved version of the silver fir reference assembly, and large European Union-funded projects such as GenTree and FORGENIUS have produced publicly accessible probe sets and SNP panels for targeted sequencing. Under the OptFORESTS project, multi-species, multi-site common gardens are being planted in several European countries, including an alpine-type garden with silver fir and European larch at four locations: two in the Alps, one in the Pyrenees and one in the Czech Republic. The authors expect these new resources and experimental sites to stimulate research on mountainous conifers in the coming years.

The article’s central message is that identifying associations between genomic, phenotypic and environmental data is no longer enough. To inform climate-resilient management of mountain forests, the field must move toward understanding the mechanisms underlying adaptation, for example by integrating ecophysiological and epigenetic studies that can separate genetic adaptation from phenotypic plasticity in long-lived trees. One promising interdisciplinary direction highlighted in the paper is dendrogenomics, which links genomic information from individual trees to retrospective functional traits recorded in tree rings, such as annual growth, extreme climatic events and water-use efficiency. Yet the survey found little present or planned focus on such interdisciplinary work among network members, possibly because collecting trait-related datasets in mountainous terrain is difficult. The authors argue that collaborative efforts spanning genomics, ecology, forest science, dendrochronology, climatology and bioinformatics are essential to build robust conservation and management strategies for vulnerable mountain forest ecosystems, and about half of surveyed members already see the field’s insights as a way to guide forest management and identify future genetic conservation units in Europe.

Subject of Research: Bibliometric analysis and researcher survey of alpine forest genomics research on seven European conifer species from 2000 to 2024

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

Article References: Budde, K. B., Köbölkuti, Z. A., Hanika, T., Heinze, B., Krutovsky, K. V., Müller, N. A., Neale, D. B., Westergren, M., & Rellstab, C. (2026). Alpine forest genomics—advances in the research field and perspectives ahead. Annals of Forest Science, 83(1), Article 50. https://doi.org/10.1186/s13595-026-01366-2

Image Credits: AI Generated

DOI: 10.1186/s13595-026-01366-2

Keywords: alpine forest genomics, climate adaptation, conifers, Norway spruce, population genetics, genomic resources, AForGeN, bibliometric analysis, dendrogenomics, mountain forests, reference genome, common gardens