Biology subjects

Zhang, B.-W.

Publications and source records attributed to Zhang, B.-W..

3 recordsLinked to original sources

bioRxiv2026

Hybrid speciation and ghost ancestry shape the Anopheles gambiae species complex

Speciation within reticulate radiations can involve both lineage divergence and hybrid lineage formation, yet recurrent introgression obscures both histories. In the Anopheles gambiae complex, gene-family presence-absence data yielded a species tree favored over four sequence-derived alternatives by network-model comparison. D-BPP analyses recovered seven reticulation events, including multiple ghost-lineage contributions, and supported a ghost-mediated hybrid origin of A. merus. Simulations showed that sampled-parent hybrid origin generates temporal convergence between reticulation and lineage formation when analyzed under an ordinary introgression model; this signature supported hybrid speciation in A. gambiae. Loci with contrasting parental affinities contained olfactory and cuticular genes with potential roles in prezygotic isolation. Together, these results resolve species relationships and identify candidate genomic mechanisms through which hybridization may have contributed to reproductive isolation.

evolutionary biology↗

bioRxiv2025

Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in Panthera and Thuja

Hybridization involving extinct or unsampled ("ghost") lineages profoundly influences species evolutionary histories, but detecting such introgression remains methodologically challenging. We introduce D-BPP, a novel framework that integrates the heuristic D-statistic (or ABBA-BABA test) with Bayesian phylogenomic inference (implemented in BPP) to efficiently infer phylogenetic networks. In D-BPP, we first employ the D-statistic to rapidly identify candidate introgression events on a predefined binary species tree; then we leverage the Bayesian test in BPP to rigorously validate these candidates and sequentially add them to the species tree, retaining only those events with strong statistical support. If the species tree is ambiguous, D-BPP identifies the most probable tree by evaluating competing topologies through Bayesian model comparison of their corresponding introgression models. Critically, our framework excels at detecting ghost introgression, which is often unidentifiable or overlooked by existing methods-- whether heuristic or full-likelihood. Applied to genomic datasets from Panthera (big cats) and Thuja (conifers), D-BPP uncovered previously undetected ghost introgression events in both clades, underscoring the pervasive role ghost lineages have played across diverse taxa. By uniquely combining the computational efficiency of heuristic D-statistics with the robust statistical rigor of full-likelihood Bayesian inference, D-BPP deciphers complex hybridization patterns obscured by conventional methods, providing a powerful tool for accurately reconstructing phylogenetic networks.

evolutionary biology↗

bioRxiv2025

Uncovering the Genetic Basis of Heterodichogamy in Pterocarya and Cyclocarya Using a Low-Input Pan-Genomic Approach

The heterodichogamous mating system, characterized by two distinct mating types (protogyny and protandry), is rare among flowering plants, but it is present in nearly all species in Juglandaceae (the walnut family). Recent studies have identified distinct structural variations underlying heterodichogamy in Juglans and Carya. To verify the independent origins of this trait in Juglandaceae and investigate whether structural variations also drive heterodichogamy in Juglans closely related genera, we explored its genetic basis in Pterocarya and Cyclocarya. Using a pan-genome graph approach, we identified a structural variation region associated with mating types across the Pterocarya genus. This region includes 30 kb tandem repeats in the dominant allele and an insertion in the recessive allele, with shared polymorphisms spanning 78 kb from the 3'UTR of S12e, covering a FAF-like gene, to a Gypsy transposable element. Downstream analyses suggest that the specific expression of FAF-like gene and small RNAs uniquely expressed from the tandem repeats of dominant allele regulate heterodichogamy. Further investigation in Cyclocarya identified nine candidate loci associated with heterodichogamy, which are non-homologous regions with those found in Pterocarya, Juglans, and Carya. These findings provide novel evidence for the multiple independent originations of convergent genetic basis in regulating heterodichogamy in Juglandaceae and highlight the utility of pan-genome approaches in deciphering structural variation-associated traits.

evolutionary biology↗