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Safeguarding Earth’s tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17% and top 50% of tree priority areas. We find that an average of 50.2% of a tree species’ range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17% and 50% priority thresholds would increase the average protected proportion of each tree species’ range to 65.5% and 82.6%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for >46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.

The idea that tropical forest and savanna are alternative states is crucial to how we manage these biomes and predict their future under global change. Large-scale empirical evidence for alternative stable states is limited, however, and comes mostly from the multimodal distribution of structural aspects of vegetation. These approaches have been criticized, as structure alone cannot separate out wetter savannas from drier forests for example, and there are also technical challenges to mapping vegetation structure in unbiased ways. Here, we develop an alternative approach to delimit the climatic envelope of the two biomes in Africa using tree species lists gathered for a large number of forest and savanna sites distributed across the continent. Our analyses confirm extensive climatic overlap of forest and savanna, supporting the alternative stable states hypothesis for Africa, and this result is corroborated by paleoecological evidence. Further, we find the two biomes to have highly divergent tree species compositions and to represent alternative compositional states. This allowed us to classify tree species as forest vs. savanna specialists, with some generalist species that span both biomes. In conjunction with georeferenced herbarium records, we mapped the forest and savanna distributions across Africa and quantified their environmental limits, which are primarily related to precipitation and seasonality, with a secondary contribution of fire. These results are important for the ongoing efforts to restore African ecosystems, which depend on accurate biome maps to set appropriate targets for the restored states but also provide empirical evidence for broad-scale bistability.

Aim Overstorey tree species influence both soil properties and microclimate conditions in the forest floor, which in turn can induce changes in ground bryophyte communities. The aim of the study was to investigate the effect of tree species identity and the most important habitat factors influencing understorey bryophytes. Methods We assessed the effect of 14 tree species and related habitat parameters, including soil parameters, vascular plant presence and light intensity on bryophytes in monospecific plots covered by nearly fifty-year-old trees in the Siemianice Experimental Forest (Poland). Results The canopy tree species determined bryophyte species richness and cover. The strongest differences were observed between plots with deciduous and coniferous trees. Soils with a more acidic pH and lower content of macronutrients supported larger bryophyte coverage. We also found a positive correlations between vascular plants and availability of light as well as bryophyte species richness. Conclusion Tree species identity and differences in habitat conditions in the forest floor lead to changes of ground bryophyte richness, cover and species composition. Consequently, the changes in the dominant tree species in the stand may result in significant repercussions on ground bryophyte communities. We indicated that the introduction of alien tree species, i.e. Quercus rubra , has an adverse effect on bryophyte communities and suggested that the selection of tree species that contribute to the community consistent with the potential natural vegetation is highly beneficial for maintaining ground bryophyte biodiversity.

We explored tree species diversity effects on soil C stock, C/N ratio, and pH as compared with effects of tree species identity. We sampled forest floors and mineral soil (0–40 cm) in a diversity gradient of 1–5 tree species composed of conifers and broadleaves in Białowieża Forest, Poland. Diversity was a weaker driver than identity of soil C stocks, C/N ratio, and pH in the soil profile. However, there were significant non-additive effects of diversity and significant effects of identity on C stock and C/N ratio within different parts of the soil profile. More diverse forests had higher C stocks and C/N ratios in the 20–40 cm layer, whereas identity in terms of conifer proportion increased C stocks and C/N ratios only in forest floors. A positive relationship between C stocks and root biomass in the 30–40 cm layer suggested that belowground niche complementarity could be a driving mechanism for higher root carbon input and in turn a deeper distribution of C in diverse forests. Diversity and identity affected soil pH in topsoil with positive and negative impacts, respectively. More diverse forests would lead to higher soil nutrient status as reflected by higher topsoil pH, but there was a slight negative effect on N status as indicated by higher C/N ratios in the deeper layers. We conclude that tree species diversity increases soil C stocks and nutrient status to some extent, but tree species identity is a stronger driver of the studied soil properties, particularly in the topsoil.

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.

In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host–microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.

The estimation of species trees (phylogenies) is one of the most important problems in evolutionary biology, and recently, there has been greater appreciation of the need to estimate species trees directly rather than using gene trees as a surrogate. A Bayesian method constructed under the multispecies coalescent model can consistently estimate species trees but involves intensive computation, which can hinder its application to the phylogenetic analysis of large-scale genomic data. Many summary statistics–based approaches, such as shallowest coalescences (SC) and Global LAteSt Split (GLASS), have been developed to infer species phylogenies for multilocus data sets. In this paper, we propose 2 methods, species tree estimation using average ranks of coalescences (STAR) and species tree estimation using average coalescence times (STEAC), based on the summary statistics of coalescence times. It can be shown that the 2 methods are statistically consistent under the multispecies coalescent model. STAR uses the ranks of coalescences and is thus resistant to variable substitution rates along the branches in gene trees. A simulation study suggests that STAR consistently outperforms STEAC, SC, and GLASS when the substitution rates among lineages are highly variable. Two real genomic data sets were analyzed by the 2 methods and produced species trees that are consistent with previous results.

The objective of this study was to verify the accuracy of tree species identification using deep learning with leaf images of broadleaf and coniferous trees in outdoor photographs. For each of 12 broadleaf and eight coniferous tree species, we acquired 300 photographs of leaves and used those to produce 72,000 256 × 256-pixel images. We used Caffe as the deep learning framework and AlexNet and GoogLeNet as the deep learning algorithms. We constructed four learning models that combined two learning patterns: one for individual classification of 20 species and the other for two-group classification (broadleaf vs. coniferous trees), with and without data augmentation, respectively. The performance of the proposed model was evaluated according to the MCC and F-score. Both classification models exhibited very high accuracy for all learning patterns; the highest MCC was 0.997 for GoogLeNet with data augmentation. The classification accuracy was higher for broadleaf trees when the model was trained using broadleaf only; for coniferous trees, the classification accuracy was higher when the model was trained using both tree types simultaneously than when it was trained using coniferous trees only.

Riparian zones within watersheds serve as vital interfaces between terrestrial and aquatic ecosystems, supporting key ecological and environmental processes. Despite their critical importance, these ecosystems are increasingly threatened by human activities. This study evaluated tree species diversity and estimated carbon density in the riparian zones downstream of the Andanan River Watershed Forest Reserve through a systematic sampling method conducted across 12 plots. Two hundred and eighty-eight individual trees were recorded, encompassing 32 species from 17 families and 27 genera. The tree population included 19 native and 13 non-native species, with five native species endemic to the Philippines. Notably, eight species identified are listed on the Philippine or IUCN Red Lists of Threatened Species. The Shannon-Wiener Diversity Index (H’=2.76) indicated moderate species diversity, while the estimated carbon content was 83.15 ± 17.49 MgC ha -1 . Geographic Information System (GIS) and Remote Sensing (RS) analysis revealed that 1,525.305 hectares of the protected area, including approximately 729.07 hectares of riparian zones, have been converted into industrial tree plantations, leading to the displacement of natural forest species. These findings underscore the urgent need for policy interventions to restore a balance between natural and plantation species in protected areas, thereby preserving biodiversity, enhancing carbon sequestration and mitigating the impacts of climate change.

Studies of biodiversity–ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community‐weighted mean trait value (CWM), and tree identity. The site was a 4‐year‐old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community‐level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroResp™ system, respectively. The relationship between tree species richness and glucose‐induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR]), with higher biomass (glucose‐induced respiration [GIR]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity—leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified functional traits related to life‐history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR. We demonstrate that both tree diversity and identity (species and functional identity—leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified functional traits related to life‐history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.