Biology subjects

Zhu, C.-D.

Publications and source records attributed to Zhu, C.-D..

8 recordsLinked to original sources

bioRxiv2026

Functional niche attributes shape species interaction roles in ecological networks

Identifying how species interact in ecological networks is key to understanding species' contributions to ecosystem functioning, but can be difficult to establish in species-rich communities. Functional niches, which capture broader ecological strategies, are often easier to assess and could help approximate species' interaction roles. We tested this by integrating species interaction and leaf functional trait data of tree species and leaf-associated interaction types from a large-scale forest biodiversity experiment. We found that identity, variability, and similarities of functional niches shaped corresponding aspects of interaction roles. Interestingly, however, this association inversed in the case of functional niche variability, which decreased instead of increased the variability of species interactions. This suggests a potential trade-off between processes that determine variability in functional and interaction space. Furthermore, effects were not constrained within aspects, with similarities of interactions being particularly responsive to most tested niche aspects, indicating that interaction-based competition among plants is particularly sensitive to functional niche differences. Moreover, many effects of functional niches depended on tree species biomass and tree species richness, highlighting the importance of the larger ecological context for determining species interaction roles. Together, our findings show that species' interaction roles, while clearly altered by, are not simply a consequence of functional niches. Instead, interaction roles integrate multiple aspects of functional niches depending on species performances and community composition and can therefore be crucial for anticipating ecosystem change.

ecology↗

bioRxiv2026

Multitrophic interaction networks mediate biodiversity effects on ecosystem multifunctionality

Biodiversity loss threatens the multifunctionality of ecosystems on which human well-being ultimately depends. Changes in multitrophic species interactions may be key to explaining the ecological consequences of biodiversity loss, but research explicitly linking species interactions and ecosystem multifunctionality remains rare. To assess interaction-mediated biodiversity effects and underlying mechanisms, characterizing the structure of species interaction networks is invaluable. Using comprehensive species interaction and ecosystem functioning data from a large-scale tree biodiversity experiment, we find consistent effects of the structure of species interaction networks on ecosystem multifunctionality across multiple types of antagonistic and mutualistic interactions. While positive effects of network size align with expected positive effects of multitrophic species diversity, positive effects of niche overlap among interacting species and negative effects of highly connected species (i.e. high linkage density) reveal additional, interaction-mediated drivers of multifunctionality. Specifically, the effects of niche overlap suggest benefits of functionally similar species, and the effects of linkage density underscore the importance of specialized interactions in promoting ecosystem multifunctionality. These findings emphasize that to effectively safeguard ecosystem service provisioning, ecosystem management and biodiversity conservation not only need to account for biodiversity changes at multiple trophic levels, but also explicitly for how species interact among each other.

ecology↗

bioRxiv2026

Cavity-nesting bees combine forest nesting habitats with surrounding floral resources in a subtropical forest diversity experiment

Wild bees face declines, and forests may serve as critical habitats for pollinators. However, how forest composition and the associated floral environment shape pollen provisioning and resource partitioning among cavity-nesting bees remains poorly understood. Here, we leveraged BEF-China, a large-scale subtropical forest biodiversity experiment with experimentally controlled plant (tree and shrub) communities, to investigate how forest composition and spatial context shape pollen provisioning, resource partitioning, and reproductive success of cavity-nesting bees. We used DNA metabarcoding to analyze floral composition of pollen provisioned by five cavity-nesting bee species, with samples collected from BEF-China across three years (2022- 2024). By comparing pollen taxonomic composition from whole-nest pooled samples and individual brood-cell samples with the experimentally planted species pool, we characterized dietary patterns and temporal dynamics of five bee species. Bees primarily relied on floral resources from the surrounding landscape, with planted trees providing essential but temporally restricted pollen supplements during specific phenological stages. Co-occurring bee species exhibited staggered nesting phenology and distinct dietary preferences for different plant families, with fine-scale resource differentiation even during periods of phenological overlap. Our results suggest that managed forests support cavity-nesting bees by providing critical woody floral resources during specific phenological gaps and offering stable nesting environments. To mitigate pollinator declines, forest management should prioritize maintaining diverse, phenologically complementary flowering vegetation within and surrounding forest stands. This ensures temporal continuity of pollen availability throughout the nesting season, which is particularly crucial for restoring pollinator services in simplified forest landscapes.

ecology↗

bioRxiv2026

Moisture reduces saproxylic bee, wasp, and parasitoid diversity in lying and standing deadwood

Saproxylic insect community assembly is structured by deadwood and forest habitat gradients, as well as biotic interactions such as competition, predation, and parasitism. However, co-variation between abiotic and biotic conditions limits our ability to disentangle their contributions. Furthermore, a focus on beetles in temperate and boreal forests has left important taxonomic and geographic knowledge gaps. Here, we tested how experimentally manipulated tree diversity, deadwood position (lying vs. standing), and biotic interactions with a dominant antagonist (ant exclusion) structure communities of deadwood-cavity-nesting bees, wasps, and their parasitoids in a subtropical forest. Lying deadwood supported less diverse and abundant communities than standing deadwood while retaining approximately twice as much moisture. Moreover, host emergence declined along moisture gradients within each deadwood type. Together, these patterns identify substrate moisture as an important factor limiting bee and wasp communities nesting in deadwood - reflecting reduced brood production, survival, or both - and as a candidate driver for their positive association with standing deadwood in forests. By contrast, neither ant exclusion nor observed ant occurrence was associated with host or parasitoid responses. Because standing deadwood is typically scarce in managed forests, our findings support retaining or creating standing deadwood structures alongside lying deadwood and, more broadly, promoting dry and elevated nesting substrates for cavity-nesting bees and wasps in conservation and restoration measures.

ecology↗

bioRxiv2025

An Eocene Origin of Passerine Birds Estimated Using Bayesian Tip Dating with Fossil Occurrences

Passerine birds are among the most diverse and species-rich groups of vertebrates, but the timescale of their evolution has been difficult to resolve with confidence. The fossil record of early passerines is relatively sparse and molecular-clock estimates of the passerine crown age have varied widely, with most previous studies relying on external fossil calibrations or assumptions relating to Gondwanan vicariance. In this study, we estimated the passerine evolutionary timescale by incorporating a set of 43 passerine fossils selected through a detailed assessment, while using a Bayesian tip-dating approach with the unresolved fossilized birth-death process. Our analyses ultimately place the passerine crown age in the Eocene, which largely closes the gap between molecular and palaeontological estimates of the passerine evolutionary timescale. Our date estimates are somewhat influenced by the prior probability density for the starting time of the diversification process. Through a simulation study, we show that the effect of the starting-time prior can be attenuated by the inclusion of morphological data for fossil and extant taxa. Overall, our study demonstrates that incorporating a curated, comprehensive set of fossils is effective in producing a well-resolved estimate of the passerine evolutionary timescale, while highlighting potential avenues for refining this estimate using Bayesian tip-dating analyses.

evolutionary biology↗

bioRxiv2024

Multi-dimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition

Environmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions. Especially, we lack a comprehensive understanding of the ways that biotic factors, including plant species richness, overall community phylogenetic and functional composition of consumers, and abiotic factors such as microclimate, determining host-parasitoid network structure and host-parasitoid community dynamics. To address this, we leveraged a five-year dataset of trap-nesting bees and wasps and their parasitoids collected in a highly-controlled, large-scale subtropical tree biodiversity experiment. We tested for effects of tree species richness, tree phylogenetic and functional diversity, and species and phylogenetic composition on species and phylogenetic diversity of both host and parasitoid communities and the composition of their interaction networks. We show that multiple components of tree diversity and canopy cover impacted both, species and phylogenetic composition of hosts and parasitoids. Generally, phylogenetic associations between hosts and parasitoids reflected non-randomly structured interactions between phylogenetic trees of hosts and parasitoids. Further, host-parasitoid network structure was influenced by tree species richness, tree phylogenetic diversity, and canopy cover. Our study indicates that the composition of higher trophic levels and corresponding interaction networks are determined by plant diversity and canopy cover especially via trophic links in species-rich ecosystems.

ecology↗

bioRxiv2021

Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process

Evolutionary timescales can be estimated using a combination of genetic data and fossil evidence based on the molecular clock. Bayesian phylogenetic methods such as tip dating and total-evidence dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of these diversified sampling schemes on Bayesian molecular dating under the unresolved fossilized birth-death (FBD) process, in which fossil taxa are topologically constrained but their exact placements are not inferred. We used synthetic data generated by simulation of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses show that increasing sampling density does not substantially improve divergence-time estimates under benign conditions. However, when the tree topologies were fixed to those used for simulation or when evolutionary rates varied among lineages, the performance of Bayesian tip dating improves with sampling density. By exploring three situations of model mismatches, we find that including all relevant fossils without pruning off those inappropriate for the FBD process can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have useful implications for Bayesian molecular dating in the era of phylogenomics.

evolutionary biology↗

bioRxiv2018

A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process

Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is Bayesian total-evidence dating, which involves the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. Part of its appeal stems from the fossilized birth-death process, which provides a model of lineage diversification for the prior on the tree topology and node times. However, total-evidence dating faces a number of considerable challenges, especially those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of total-evidence dating with the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses show that fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Total-evidence dating generally performs well in recovering the relationships among extant taxa, but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the origin time of the fossilized birth-death process and the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Overall, our results provide a detailed view of the performance of total-evidence dating, which will inform further development of the method and its application to key questions in evolutionary biology.

evolutionary biology↗