Biology subjects

Zhou, Q.-S.

Publications and source records attributed to Zhou, Q.-S..

3 recordsLinked to original sources

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↗