Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures.

A major topic of debate in developmental biology centers on whether development is continuous, discontinuous, or a mixture of both. Pseudo-time trajectory models, optimal for visualizing cellular progression, model cell transitions as continuous state manifolds and do not explicitly model real-time, complex, heterogeneous systems and are challenging for benchmarking with temporal models. We present a data-driven framework that addresses these limitations with temporal single-cell data collected at discrete time points as inputs and a mixture of dependent minimum spanning trees (MSTs) as outputs, denoted as dynamic spanning forest mixtures (DSFMix). DSFMix uses decision-tree models to select genes that account for variations in multimodality, skewness and time. The genes are subsequently used to build the forest using tree agglomerative hierarchical clustering and dynamic branch cutting. We first motivate the use of forest-based algorithms compared to single-tree approaches for visualizing and characterizing developmental processes. We next benchmark DSFMix to pseudo-time and temporal approaches in terms of feature selection, time correlation, and network similarity. Finally, we demonstrate how DSFMix can be used to visualize, compare and characterize complex relationships during biological processes such as epithelial-mesenchymal transition, spermatogenesis, stem cell pluripotency, early transcriptional response from hormones and immune response to coronavirus disease. Our results indicate that the expression of genes during normal development exhibits a high proportion of non-uniformly distributed profiles that are mostly right-skewed and multimodal; the latter being a characteristic of major steady states during development. Our study also identifies and validates gene signatures driving complex dynamic processes during somatic or germline differentiation.

The influence of forest types including native and non-native tree species on soil macrofauna depends on site conditions.

The ongoing climate change calls for managing forest ecosystems in temperate regions toward more drought-resistant and climate-resilient stands. Yet ecological consequences of management options such as planting non-native tree species and mixing coniferous and deciduous tree species have been little studied, especially on soil animal communities, key in litter decomposition and pest control. Here, we investigated the taxonomic and trophic structure of soil macrofauna communities in five forest types including native European beech (Fagus sylvatica), range-expanding Norway spruce (Picea abies) and non-native Douglas fir (Pseudotsuga menziesii) as well as conifer-beech mixtures across loamy and sandy sites in northern Germany. Abundance of primary decomposers (feeding predominantly on litter) was high in Douglas fir and beech forests, benefiting from less acidic soil and more favorable litter resources compared to spruce forests, while secondary decomposers (feeding predominantly on microorganisms and microbial residues) reached highest densities in spruce forests. Differences in abundance and species richness among forest types generally varied between regions and were most pronounced in Douglas fir of the sandy region. However, trophic guilds differed more between regions than between forest types, indicating that environmental factors outweigh the importance of forest type on soil macrofauna communities. The analysis of stable isotopes (δ15N and δ13C values) supported the general robustness in trophic position of macrofauna trophic guilds against variations in forest types and regions, but indicated reduced detrital shifts and food-chain lengths in coniferous compared to European beech forests with mixtures mitigating these effects. Overall, for evaluating consequences of future forest management practices on the structure and functioning of soil animal communities, regional factors need to be considered, but in particular at loamy sites the taxonomic and trophic structure of soil macrofauna communities are resistant against changes in forest types.