Biology subjects

Zhang, D.-Y.

Publications and source records attributed to Zhang, D.-Y..

11 recordsLinked to original sources

bioRxiv2026

D-plus: Beyond the D-statistic -- Accurate Detection and Characterization of Introgression Despite Among-Lineage Rate Variation

Ubiquitous in phylogenomic and population-genomic introgression work, the D-statistic has fallen victim to its own success. Its reliability is compromised by two major confounding factors: among-lineage substitution rate heterogeneity, which generates spurious signals of introgression, and unsampled "ghost" lineages, which mislead the characterization of introgression by erroneously attributing ghost ancestry to extant species. Here, we developed D-plus, a maximum-likelihood tool that explicitly accounts for both confounding factors to unpack the sources of significant D-statistic signals. Simulations demonstrate that D-plus effectively mitigates false introgression calls under among-lineage rate variation. Meanwhile, it retains high sensitivity for genuine introgression signals and correctly assigns detected signals to introgression involving ghost lineages, or solely between extant non-sister lineages, or a combination of the two. Our D-plus re-analysis of phylogenomic data from Jaltomata (Solanaceae) overturns prior interpretations of significant D-statistic signals, which were conventionally regarded as evidence for recurrent non-sister introgression. Instead, our results favor alternative explanations invoking artefacts driven by lineage-specific rate heterogeneity as well as two ghost introgression events. Collectively, D-plus addresses major methodological limitations inherent to traditional D-statistic analyses and enables accurate detection and characterization of introgression events.

bioinformatics↗

bioRxiv2026

Subgenome-Level Phylogeny Reveals an Allopolyploid Origin of Chloranthales from Ancestral Monocot and Eudicot Lineages

Angiosperms (flowering plants) represent the most species-rich lineage of land plants, yet deep phylogenetic relationships among their major clades, particularly within mesangiosperms, remain notoriously difficult to resolve. Although hybridization and whole-genome duplication (WGD) are recognized as major evolutionary forces, the contribution of ancient allopolyploidization, which combines hybridization with WGD, to deep-node phylogenetic discordance in mesangiosperms remains poorly understood. Here, we analyzed genomes from seven representative early-diverging angiosperm lineages, each containing no more than one lineage-specific WGD event. Using a comparative phylogenomic framework, we characterized WGD-derived paralogs across five WGD-bearing lineages. In contrast to other polyploid lineages, Chloranthales WGD-derived paralogs rarely formed sister relationships in gene trees. After evaluating alternative explanations, including incomplete lineage sorting, ancient paralogy, and analytical artifacts, we demonstrate that this discordant phylogenetic signal reflects the genomic legacy of an ancient allopolyploidization event. We further resolved the Chloranthales subgenomes by exploiting biased fractionation patterns within conserved syntenic regions. Subgenome-resolved phylogenomic analyses revealed that the dominant Chloranthales subgenome exhibits phylogenetic affinity with eudicots, whereas the recessive subgenome is associated with monocots, indicating a deep reticulate origin involving ancestral lineages related to these major angiosperm clades. Our findings provide subgenome-resolved evidence that ancient allopolyploidization can connect deeply diverged lineages during early angiosperm evolution, highlighting the importance of incorporating reticulate polyploid histories into phylogenomic frameworks for resolving deep evolutionary relationships.

systems biology↗

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

Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors

Recent theoretical and algorithmic advances in introgression detection, coupled with the growing availability of genome-scale data, have highlighted the widespread occurrence of interspecific gene flow across the tree of life. However, current methods largely depend on the molecular clock assumption--a questionable premise given empirical evidence of substitution rate variation across lineages. While such rate heterogeneity is known to compromise gene flow detection among divergent lineages, its impact on closely related taxa at shallow evolutionary timescales remains poorly understood, likely because these taxa are often assumed to adhere to a molecular clock. To address this gap, we combine theoretical analyses and simulations to evaluate the robustness of widely used site-pattern methods (D-statistic and HyDe) to rate variation across phylogenetic timescales. Our results demonstrate that both methods exhibit high sensitivity to even minor deviations from the molecular clock at shallow timescales, complementing previous findings at deeper scales. Specifically, in young phylogenies (with an age of 3x105 generations) with small population sizes, weak (17% difference) and moderate (33% difference) rate variation can inflate false-positive rates up to 35% and 100%, respectively, when using site-pattern counts from a 500Mb genome. Employing a more distant outgroup intensifies these spurious signals. Our study demonstrates that summary tests for introgression are pervasively vulnerable to minor rate variations and underscores the critical need for advanced methodologies to disentangle genuine introgression from false signals generated by rate heterogeneity.

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↗

bioRxiv2024

A Cautionary Note on Using STRUCTURE to Detect Hybridization in a Phylogenetic Context

Population genetic clustering methods are widely used to detect hybridization events between closely related populations within species, as well as between deeply diverged lineages across phylogenetic time-scales, although their strengths and limitations in the latter cases remain poorly explored. This study presents the first systematic evaluation of the performance of the most popular population clustering method, STRUCTURE, under a variety of cross-species hybridization scenarios, including hybrid speciation, as well as introgression involving ghost (i.e., extinct or unsampled) lineages or otherwise. Our simulations demonstrate that STRUCTURE performs well in identifying hybrids and their parental donors only when admixture happens very recently between sampled extant lineages. However, STRUCTURE generally fails to detect signals of admixture when hybridization occurs in deep time or when gene flow stems from ghost lineages. We find that symmetrical parental contribution in cases of hybrid speciation will often be revealed as extremely asymmetrical in STRUCTURE, especially when the admixture event occurred more than some time ago. Our results suggest that population-genetic clustering methods may be very inefficient for detecting either ancient or ghost admixtures, partly explaining why ghost introgression has escaped the attention of evolutionary biologists until recently.

evolutionary biology↗

bioRxiv2023

Uncovering Ghost Introgression Through Genomic Analysis of a Distinct East Asian Hickory Species

Although the possibility of introgression from ghost lineages (all unsampled extant and extinct taxa) is now widely recognized, detecting and characterizing ghost introgression remains a challenge. Here, we propose a combined use of the popular D-statistic method, which tests for the presence of introgression, and the full-likelihood method BPP, which determines which of the possible gene-flow scenarios, including ghost introgression, is truly responsible. We illustrate the utility of this approach by investigating the reticulation and bifurcation history of the genus Carya (Juglandaceae), including the beaked hickory Carya sinensis. To achieve this goal, we generated two chromosome-level reference genomes respectively for C. sinensis and C. cathayensis. Furthermore, we re-sequenced the whole genomes of 43 individuals from C. sinensis and one individual from each of the 11 diploid species of Carya. The latter dataset with one individual per species is used to reconstruct the phylogenetic networks and estimate the divergence time of Carya. Our results unambiguously demonstrate the presence of ghost introgression from an extinct lineage into the beaked hickory, dispelling certain misconceptions about the phylogenetic history of C. sinensis. We also discuss the profound implications of ghost introgression into C. sinensis for the historical biogeography of hickory species. [BPP; Carya; D-statistic; gene flow; ghost introgression]

evolutionary biology↗

bioRxiv2023

Detection of Ghost Introgression from Phylogenomic Data Requires a Full-Likelihood Approach

AO_SCPLOWBSTRACTC_SCPLOWIn recent years, the study of hybridization and introgression has made significant progress, with ghost introgression - the transfer of genetic material from extinct or unsampled lineages to extant species - emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site patterns or gene tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP using multilocus sequence alignments, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

evolutionary biology↗

bioRxiv2022

Chinese fir genome and the evolution of gymnosperms

Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families and 70 genera. Their distinctiveness has triggered much debate on their origin, evolution, and phylogenetic placement among seed plants. To better understand the evolution of gymnosperms and their relation to other seed plants, we report here a high-quality genome sequence for a tree species, Chinese fir (Cunninghamia lanceolata), which has excellent timber quality and high aluminum adaptability and is a member of Cupressaceae with high levels of heterozygosity. We assembled an 11.24 Gb genome with a contig N50 value of 2.15 Mb and anchored the 10.89 Gb sequence to 11 chromosomes. Phylogenomic analyses showed that cycads sister to Ginkgo, which place to sister in all gymnosperm lineages, and Gnetales within conifers sister to Pinaceae. Whole-genome duplication (WGD) analysis showed that the ancestor of seed plants has differentiated into angiosperms and gymnosperms after having experienced a WGD event. The ancestor of extant gymnosperm has experienced a gymnosperm-specific WGD event and the extant angiosperms do not share a common WGD before their most recent common ancestor diverged into existing angiosperms lineages. Analysis of the MADS-box gene family of C. lanceolata revealed the developmental mechanism of the reproductive organs in C. lanceolata, which supported the (A)B(C) model of the development of gymnosperms reproductive organs. In addition, astringent seeds and shedding of whole branches (with withered leaves) might be a strategy of C. lanceolata that evolved during long-term adaptation to an aluminum-rich environment. The findings also reveal the molecular regulation mechanism of shade tolerance in C. lanceolata seedlings. Our results improve the resolution of ancestral genomic features within seed plants and the knowledge of genome evolution and diversification of gymnosperms.

genomics↗

bioRxiv2022

Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time

AO_SCPLOWBSTRACTC_SCPLOWThe species studied in any evolutionary investigation generally constitute a very small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has been rarely studied and is thus poorly understood. In this study, we use mathematical analysis and simulations to examine the robustness of species tree methods based on a multispecies coalescent model under gene flow sourcing from an extant or ghost lineage. We found that very low levels of extant or ghost introgression can result in anomalous gene trees (AGTs) on three-taxon rooted trees if accompanied by strong incomplete lineage sorting (ILS). In contrast, even massive introgression, with more than half of the recipient genome descending from the donor lineage, may not necessarily lead to AGTs. In cases involving an ingroup lineage (defined as one that diverged no earlier than the most basal species under investigation) acting as the donor of introgression, the time of root divergence among the investigated species was either underestimated or remained unaffected, but for the cases of outgroup ghost lineages acting as donors, the divergence time was generally overestimated. Under many conditions of ingroup introgression, the stronger the ILS was, the higher was the accuracy of estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.

evolutionary biology↗