Genomic Diversity, Phylogeny, and Conservation of Forest Tree Species

Dear Colleagues,

Forest tree species are foundational to global ecosystems and human societies. The study of their genomic diversity, phylogeny, and conservation has evolved in tandem with technological and conceptual advances, comprising three key eras:

• Early Foundations (1980s–2000s): Research relied on neutral genetic markers (e.g., microsatellites, AFLPs) to characterize population genetic diversity and simple phylogenetic relationships.
• Genomic Revolution (2010s–2020s): The advent of next-generation sequencing (NGS) technologies (e.g., whole-genome sequencing, RAD-seq, transcriptomics) transformed the field.
• Integrative Conservation Era (2020s–present): Today, research focuses on translating genomic insights to actionable conservation. This includes predicting tree species’ adaptive responses to climate change (via genomic–environment associations), designing “genetically informed” restoration (e.g., selecting climate-resilient provenances), and addressing conservation gaps (e.g., protecting genomic diversity in rare or endangered tree species).

The primary aim of this Special Issue is to advance the interdisciplinary understanding of forest tree genomic diversity and phylogeny and to accelerate the translation of these insights into evidence-based conservation and management strategies. Its scope spans all forest tree lineages (conifers, angiosperms, ancient or endemic species) and scales (from population-level genomic variation to deep phylogenetic relationships), with a focus on bridging basic science and applied conservation. Key thematic areas include (but are not limited to) the following:

• Genomic diversity of forest trees (neutral and adaptive variation, drivers of genetic structure, impacts of fragmentation/climate on genomic integrity).
• Phylogenetic studies (high-resolution phylogenies, cryptic species discovery, evolutionary diversification of forest tree lineages). Leveraging whole-genome sequencing or ultra-conserved elements (UCEs) to resolve long-standing phylogenetic ambiguities and detect cryptic species.
• Adaptive Genomics for Climate Resilience: Using genomic-environment associations (GEAs) and polygenic risk scores to identify tree populations with genetic potential to tolerate future climate conditions (e.g., heat, drought) and integrating these data into “climate-smart” restoration.
• Phylogenetic Diversity (PD) in Conservation Planning: Using phylogenies to quantify PD (evolutionary uniqueness) and prioritize areas for protection (e.g., hotspots of PD in tropical rainforests) to preserve not just species, but evolutionary potential.
• Genomic tools for conservation practice and Genomic Monitoring of Rare/Endangered Species: Applying low-cost NGS tools (e.g., environmental DNA, or eDNA) to assess genomic diversity in hard-to-sample species (e.g., ancient trees, fragmented populations) and track changes over time.
• Challenges in forest tree genomics (e.g., large genome sizes, long generation times) and innovative solutions.

Dr. Federico Sebastiani
Dr. Alexis Marchesini
Guest Editors

Dr. Sara Villa
Guest Editor Assistant

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

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