Biology subjects

Zhang, Y. M.

Publications and source records attributed to Zhang, Y. M..

16 recordsLinked to original sources

bioRxiv2026

Olfactory-mediated host tracking and rapid local adaptation in a seed-feeding wasp

Understanding how specialized herbivores track divergence among their hosts is central to evolutionary biology. Congruent genetic structure between hosts and herbivores is often interpreted as evidence of long-term codivergence, but similar patterns may also arise when herbivores rapidly adapt to pre-existing host differentiation. Here, we integrate population genomics, host volatile profiling, and behavioral assays to examine host-associated divergence in the obligate seed-feeding wasp Megastigmus daduheensis and its conifer host Cupressus chengiana across three river valleys on the eastern Qinghai-Tibet Plateau. Despite strong phylogeographic congruence between each of the three wasp and host lineages, calibrated demographic analyses indicate that wasp divergence occurred during the early Holocene, substantially later than the Pliocene-Pleistocene divergence of host lineages. This temporal mismatch is inconsistent with strict long-term codivergence and instead supports rapid host tracking in a topographic complex region. Host lineages differed in volatile organic compound profiles, and behavioral assays showed that wasps were preferentially attracted to volatiles from their local host lineages. These results identify olfactory-mediated host recognition as a plausible mechanism promoting host fidelity and reinforcing host-associated genomic and behavioral differentiation. Our findings show that apparently concordant host-herbivore divergence can emerge over compressed evolutionary timescales through rapid local adaptation, highlighting how ecological differentiation can accumulate within species through host tracking.

evolutionary biology↗

bioRxiv2026

The chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

Gall-inducing wasps are emerging models for studying plantinsect coevolution, host manipulation, host plant adaptation, and speciation, yet chromosome-level resources remain scarce for most lineages. The blueberry stem gall wasp (BSGW), Hemadas nubilipennis (Hymenoptera: Ormyridae), is native to North America where it induces galls on both lowbush (Vaccinium angustifolium) and highbush blueberries (V. corymbosum). Recently, BSGW has reached outbreak densities in cultivated highbush production. Given that (a) the biology has been characterized primarily from natural lowbush-associated populations, (b) the absence of genomic resources limits comparative analyses, and (c) populations on cultivated highbush represent a recent host shift, we generated the first chromosome-level genome from wild lowbush blueberry. The BSGW genome consists of five chromosome-scale scaffolds totaling 1.08 Gb (N50 = 218 Mb), the second largest known in Chalcidoidea. Comparative analysis reveals that genome size variation is driven primarily by transposable element proliferation (R = 0.96, p < 0.001), with BSGW exhibiting a high proportion of unclassified TEs. Gene-body methylation is conserved, enriched in exons of broadly expressed core genes, and correlates with gene density. The mitochondrial genome (18,697 bp) exhibits extensive gene rearrangement, and COI sequences reveal 4.35.4% divergence from geographically distant populations, suggesting a complex of cryptic species. Additionally, we assemble a near-complete genome of the endosymbiont Wolbachia pipientis (Supergroup A), which encodes PifA and PifB effectors potentially linked to parthenogenesis. These resources establish a foundation for population genomics, taxonomic revision, and applied management, while providing insights into genome architecture, epigenetics, and symbiont interactions.

genomics↗

bioRxiv2026

Chromosome-level genome assembly of the Erythrina Gall Wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae)

The erythrina gall wasp, Quadrastichus erythrinae, is an invasive gall-inducing chalcidoid wasp and a major pest of the endemic wiliwili tree (Erythrina sandwicensis) in Hawai{square}i. As a foundation to associated research, we generated a chromosome-level genome assembly from a wild-collected female measuring <2 mm. The final assembly consists of five scaffolds representing the five autosomes totaling 399 Mb (N50 = 75.6 Mb) and one unplaced 16 kb contig. BUSCO analysis recovers 91.1% of conserved Hymenoptera orthologs, representing the first chromosome-scale genome for the genus Quadrastichus. Comparative genomic analyses reveal syntenic conservation across Hymenoptera despite deep evolutionary divergence, with strongest collinearity to the chalcidoid Nasonia vitripennis. Genome size variation is largely explained by repeat content, and Q. erythrinae exhibits high proportions of unclassified transposable elements similar to the cynipid gall inducer. We also assembled a complete genome of its endosymbiont, Wolbachia pipientis. Together, these genomic resources provide a foundation for comparative, evolutionary, and applied research aimed at managing this invasive pest.

genomics↗

bioRxiv2025

Phasing in and out of phytophagy: phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements

We present the first global molecular phylogenetic hypothesis for the family Eurytomidae, a group of chalcidoid wasps with diverse biology, with a representative sampling (197 ingroups and 11 outgroups) that covers all described subfamilies, and 70% of the known genera. Analyses of 962 Ultra-Conserved Elements (UCEs) with concatenation (IQ-TREE) and multispecies coalescent approaches (ASTRAL) resulted in highly supported topologies in recovering the monophyly of Eurytomidae and its four subfamilies. The taxonomy of Eurytomidae, and in particular the large subfamily Eurytominae, needs major revisions as most large genera are recovered as para- or polyphyletic, and the erection of multiple new genera is required in the future to accommodate these taxa. Here, we synonymize the genera Cathilaria (C. certa, C. globiventris, C. opuntiae, and C. rigidae) and the monotypic Aiolomorphus rhopaloides within Tetramesa syn. nov., Parabruchophagus (P. kazakhstanicus, P. nikolskaji, P. rasnitsyni, P. saxatilis, and P. tauricus) and Exeurytoma (E. anatolica, E. caraganae, and E. kebanensis) within Bruchophagus syn. nov.. We also provide 137 DNA barcode COI fragments extracted from the UCE contigs to aid in future identifications of Eurytomidae using this popular genetic marker. Eurytomidae most likely originated in South America with an estimated crown age of 83.37 Ma. Ancestral state reconstruction indicates that secondary phytophagy has evolved at least seven times within the subfamily Eurytominae, showcasing the evolutionary flexibility of these vastly understudied wasps.

zoology↗

bioRxiv2024

Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants

While some relationships in phylogenomic studies have remained stable since the era of Sanger sequencing, many challenging nodes elude resolution, even with genome-scale data. As early studies grappled with random error and insufficient information, incongruence or lack of resolution in phylogenomics is generally associated with inadequate modeling of biological phenomena combined with analytical issues leading to systematic biases. Few phylogenomic studies, however, explore the potential for random error or establish an expectation of what level of resolution should be expected from a given empirical dataset. In presenting incongruent results, phylogeneticists face a choice of providing a diverse array of results from different approaches or a single preferred tree, with few attempting to integrate uncertainties across methods. Recent phylogenetic work has uncovered many well-supported and often novel relationships, as well as more contentious findings, across the phylogeny of ants. Ants are the most species-rich lineage of social insects and among the most ecologically important terrestrial animals. As a result, they have attracted much research, including regarding systematics. To date, however, there has been no comprehensive genus-level phylogeny of the ants inferred using genomic data combined with an effort to evaluate signal and incongruence throughout. Here we provide deeper insight into and quantify uncertainty across the ant tree of life. We accomplish this with the most taxonomically comprehensive Ultraconserved Elements dataset to date, including 277 (81%) of recognized ant genera from all 16 extant subfamilies, representing over 98% of described species-level diversity. We use simulations to establish expectations for resolution, identify branches with less-than-expected concordance, and dissect the effects of data and model selection on recalcitrant nodes. We also construct a consensus tree integrating uncertainty from multiple analyses. Simulations show that hundreds of loci are needed to resolve recalcitrant nodes on our genus-level ant phylogeny, even under a best-case scenario of known model parameters and without systematic bias. This demonstrates that random error continues to play a role in phylogenomics. Our analyses provide a comprehensive picture of support and incongruence across the ant phylogeny, and our consensus topology is congruent with a recent phylogenomic study on the subfamily-level, while rendering a more realistic picture of uncertainty and significantly expanding generic sampling. We use this topology for divergence dating and find that assumptions about root age have significant impact on the dates inferred. Our results suggest that improved understanding of ant phylogeny will require both more data and better phylogenetic models. We also provide a workflow to identify under-supported nodes in concatenation analyses, outline a pragmatic way to reconcile conflicting results in phylogenomics, and introduce a user-friendly locus selection tool for divergence dating.

evolutionary biology↗

bioRxiv2024

Phylogenetic and non-phylogenetic patterns in the richness, frequency and composition of links in a herbivore-parasitoid interaction network

Revealing processes that structure species interactions is central to understanding community assembly and dynamics. Species interact via their phenotypes, but identifying and quantifying the traits that structure species-specific interactions (links) can be challenging. Where these traits show phylogenetic signal, however, link properties may be predictable using models that incorporate phylogenies in place of trait data. We analysed variation in link richness, frequency, and species identity in a multi-site dataset of interactions between oak cynipid galls and parasitoid natural enemies, using a Bayesian mixed modelling framework allowing concurrent fitting of phylogenetic effects of both trophic levels. In both link incidence (presence/absence) and link frequency datasets, we identified strong signatures of cophylogeny (related parasitoids attack related host galls) alongside patterns independent of either phylogeny. Our results are robust to simulations of substantially reduced sample completeness, and are consistent with the structuring of trophic interactions by a combination of phylogenetically conserved and convergently evolving traits in both trophic levels. We discuss our results in light of phenotypic traits thought to structure gall-parasitoid interactions and consider wider applications of this approach, including inference of underlying community assembly processes and prediction of economically important trophic interactions.

ecology↗

bioRxiv2023

Phylogenomic Insights into the Evolution and Origin of Nematoda

The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to eight nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is well-resolved across most clades, with topologies remaining consistent across various reconstruction parameters. The subclass Enoplia is placed as a sister group to the rest of Nematoda, agrees with previous published phylogenies. While the order Triplonchida is monophyletic, it is not well-supported, and the order Enoplida is paraphyletic. Taxa possessing a stomatostylet form a monophyletic group; however, the superfamily Aphelenchoidea does not constitute a monophyletic clade. The genera Trichinella and Trichuris are inferred to have shared a common ancestor approximately 202 mya, a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated [~]305 mya, corresponding to the transition from the Devonian to the Permian period. The genus Thornia is placed outside of Dorylaimina and Nygolaimina, disagreeing with its position in previous studies. Additionally, we tested the whole genome amplification method and demonstrated that it is a promising strategy for obtaining sufficient DNA for phylogenomic studies of microscopic eukaryotes. This study significantly expanded the current nematode genome dataset, and the well-resolved phylogeny enhances our understanding of the evolution of Nematoda.

genomics↗

bioRxiv2023

The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. In human cells, the interferon induced Myxovirus resistance protein 1 (MxA) binds to NP and restricts influenza replication. This selection pressure has caused NP to evolve a few critical MxA-resistant mutations, particularly the highly conserved Pro283 substitution. Previous work showed that this essential Pro283 substitution impairs influenza growth, and the fitness defect becomes particularly prominent at febrile temperature (39 {degrees}C) when host chaperones are depleted. Here, we biophysically characterize Pro283 NP and Ser283 NP to test if the fitness defect is owing to Pro283 substitution introducing folding defects. We show that the Pro283 substitution changes the folding pathway of NP without altering the native structure, making NP more aggregation prone during folding. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape. TeaserPro283 substitution in flu nucleoprotein introduces folding defects, and makes influenza uniquely dependent on host chaperones.

biophysics↗

bioRxiv2023

Speciation in kleptoparasites of oak gall wasps often correlates with shifts into new tree habitats, tree organs, and gall morphospace

Host shifts to new plants can drive speciation for plant-feeding insects, but how commonly do host shifts also drive diversification for the parasites of those same insects? Oak gall wasps induce galls on oak trees and shifts to novel tree hosts and new tree organs have been implicated as drivers of oak gall wasp speciation. Gall wasps are themselves attacked by many insect parasites, which must find their hosts on the correct tree species and organ, but which also must navigate the morphologically variable galls with which they interact. Thus, we ask whether host shifts to new trees, organs, or gall morphologies correlate with gall parasite diversification. We delimit species and infer phylogenies for two genera of gall kleptoparasites, Synergus and Ceroptres, reared from a variety of North American oak galls. We find that most species were reared from galls induced by just one gall wasp species, and no parasite species was reared from galls of more than four species. Most kleptoparasite divergence events correlate with shifts to non-ancestral galls. These shifts often involved changes in tree habitat, gall location, and gall morphology. Host shifts are thus implicated in driving diversification for both oak gall wasps and their kleptoparasitic associates.

evolutionary biology↗

bioRxiv2022

The arthropod associates of 155 North American cynipid oak galls

The identities of most arthropod associates of cynipid-induced oak galls in the western Palearctic are generally known. However, a comprehensive accounting of associates has been performed for only a small number of the galls induced by the estimated 700 species of cynipid gall wasp in the Nearctic. This gap in knowledge stymies many potential studies of diversity, coevolution, and community ecology, for which oak gall systems are otherwise ideal models. We report rearing records of insects and other arthropods from more than 527,306 individual galls representing 201 different oak gall types collected from 32 oak tree species in North America. Of the 201 gall types collected, 155 produced one or more animals. A total of 151,075 animals were found in association with these 155 gall types, and of these 61,044 (40.4%) were gall wasps while 90,031 (59.6%) were other arthropods. We identified all animals to superfamily, family, or, where possible, to genus. We provide raw numbers and summaries of collections, alongside notes on natural history, ecology, and previously published associations for each taxon. For eight common gall-associated genera (Synergus, Ceroptres, Euceroptres, Ormyrus, Torymus, Eurytoma, Sycophila, and Euderus), we also connect rearing records to gall wasp phylogeny, geography, and ecology - including host tree and gall location (host organ), and their co-occurrence with other insect genera. Though the diversity of gall wasps and the large size of these communities is such that many Nearctic oak gall-associated insects still remain undescribed, this large collection and identification effort should facilitate the testing of new and varied ecological and evolutionary hypotheses in Nearctic oak galls.

zoology↗

bioRxiv2022

Speciation in Nearctic oak gall wasps is frequently correlated with changes in host plant, host organ, or both.

Quantifying the frequency of shifts to new host plants within diverse clades of specialist herbivorous insects is critically important to understand whether and how host shifts contribute to the origin of species. Oak gall wasps (Hymenoptera: Cynipidae: Cynipini) comprise a tribe of ~1000 species of phytophagous insects that induce gall formation on various organs of trees in the family Fagacae, -- primarily the oaks (genus Quercus; ~435 sp). The association of oak gall wasps with oaks is ancient (~50 my), and most oak species are galled by one or more gall wasp species. Despite the diversity of both gall wasp species and their plant associations, previous phylogenetic work has not identified a strong signal of host plant shifting among oak gall wasps. However, most emphasis has been on the Western Palearctic and not the Nearctic where both oaks and oak gall wasps are considerably more species rich and where oaks are more phylogenetically diverse. We collected 86 species of Nearctic oak gall wasps from 10 of the 14 major clades of Nearctic oaks and sequenced >1000 Ultra Conserved Elements (UCEs) and flanking sequences to infer wasp phylogenies. We assessed the relationships of Nearctic gall wasps to one another and, by leveraging previously published UCE data, to the Palearctic fauna. We then used phylogenies to infer historical patterns of shifts among host tree species and tree organs. Our results indicate that oak gall wasps have moved between the Palearctic and Nearctic at least four times, that some Palearctic clades have their proximate origin in the Nearctic, and that gall wasps have shifted within and between oak tree sections, subsections, and organs considerably more often than the analysis of previous data have suggested. Given that host shifts have been demonstrated to drive reproductive isolation between host-associated populations in other phytophagous insects, our analyses of Nearctic gall wasps suggest that host shifts are key drivers of speciation in this clade, especially in hotspots of oak diversity. Though formal assessment of this hypothesis requires further study, two putatively oligophagous gall wasp species in our dataset show signals of host-associated genetic differentiation unconfounded by geographic distance, suggestive of barriers to gene flow associated with the use of alternative host plants.

evolutionary biology↗

bioRxiv2022

Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data

Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.

evolutionary biology↗

bioRxiv2021

Ormyrus labotus Walker (Hymenoptera: Ormyridae): another generalist that should not be a generalist is not a generalist

Several recent reappraisals of supposed generalist parasite species have revealed hidden complexes of species, each with considerably narrower host ranges. Parasitic wasps that attack gall-forming insects on plants have life history strategies that are thought to promote specialization, and though many species are indeed highly specialized, others have been described as generalist parasites. Ormyrus labotus Walker (Hymenoptera: Ormyridae) is one such apparent generalist, with rearing records spanning more than 65 host galls associated with a diverse set of oak tree species and plant tissues. We pair a molecular approach with morphology, host ecology, and phenological data from across a wide geographic sample to test the hypothesis that this supposed generalist is actually a complex of several more specialized species. We find 16-18 putative species within the morphological species O. labotus, each reared from only 1-6 host gall types, though we identify no single unifying axis of specialization. We also find cryptic habitat specialists within two other named Ormyrus species. Our study suggests that caution should be applied when considering host ranges of parasitic insects described solely by morphological traits, particularly given their importance as biocontrol organisms and their role in biodiversity and evolutionary studies.

evolutionary biology↗

bioRxiv2020

Invertebrate Community Associated with the Asexual Generation of Bassettia pallida Ashmead (Hymenoptera: Cynipidae)

Cynipid gall wasps play an important role in structuring oak invertebrate communities. Wasps in the Cynipini tribe typically lay their eggs in oaks (Quercus L.), and induce the formation of a "gall", which is a tumor-like growth of plant material that surrounds the developing wasp. As the wasp develops, the cynipid and its gall are attacked by a diverse community of natural enemies, including parasitoids, hyperparasitoids, and inquilines. Determining what structures these species-rich natural enemy communities across cynipid gall wasp species is a major question in gall wasp biology. Additionally, gall wasps are ecosystem engineers, as the abandoned gall is used by other invertebrates. The gall-associated insect communities residing on live oaks (Quercus geminata Small and Q. virginiana Mill.) are emerging as a model system for answering ecological and evolutionary questions ranging from community ecology to the evolution of new species. Documenting the invertebrates associated with cynipids in this system will expand our understanding of the mechanisms influencing eco-evolutionary processes, record underexplored axes of biodiversity, and facilitate future work. Here, we present the community of natural enemies and other associates of the asexual generation of the crypt gall wasp, Bassettia pallida Ashmead. We compare the composition of this community to communities recently documented from two other cynipid gall wasps specializing on live oaks along the U.S. Gulf coast, Disholcaspis quercusvirens Ashmead and Belonocnema treatae Mayr. B. pallida and their crypts support a diverse arthropod community, including over 25 parasitoids, inquilines, and other associated invertebrates spanning 5 orders and 16 families.

ecology↗

bioRxiv2019

Phylogeny of Holarctic gall wasps of the genera Diplolepis and Periclistus (Hymenoptera: Cynipidae) based on DNA barcodes

Rose gall wasps Diplolepis induce structurally distinct galls on wild roses, which provide gallers with food and shelter. These galls are attacked by a wide variety of micro-hymenopterans including another cynipid Periclistus that act as inquilines. Both Diplolepis and Periclistus are difficult to distinguish based on adult morphology, instead the structural appearance of galls is often used to distinguish species. Using the mitochondrial gene COI, we built phylogenies of both Diplolepis and Periclistus, while also estimating the ancestral host use of the inducers. Our phylogeny recovered the monophyly of Diplolepis, which have likely diverged from single-or multi-chambered leaf gallers to other plant organs. Periclistus exhibits a divide between the Palearctic and Nearctic clades, and ranges from specialists to generalists in terms of host specificity. The molecular results have largely supported the validity of species described in the literature, with notable exceptions in four species groups. While it is premature to enact any taxonomic changes without additional molecular markers, this incongruence between morphological and molecular data indicates these groups need taxonomic revision and gall morphology alone may be inadequate to delimit species.

zoology↗

bioRxiv2018

Cancer modeling by Transgene Electroporation in Adult Zebrafish (TEAZ)

Transgenic animals are invaluable for modeling cancer genomics, but often require complex crosses of multiple germline alleles to obtain the desired combinations. Zebrafish models have advantages in that transgenes can be rapidly tested by mosaic expression, but these typically lack spatial and temporal control of tumor onset, which limits their utility for the study of tumor progression and metastasis. To overcome these limitations, we have developed a method called Transgene Electroporation in Adult Zebrafish (TEAZ). TEAZ can deliver DNA constructs with promoter elements of interest to drive fluorophores, oncogenes, or CRISPR-Cas9-based mutagenic cassettes in specific cell types. Using TEAZ, we created a highly aggressive melanoma model by expression of BRAFV600E in spatially constrained melanocytes in the context of p53 deficiency and Cas9-mediated inactivation of Rb1. Unlike prior models that take ~4 months to develop, we found that TEAZ leads to tumor onset in ~7 weeks and these develop in fully immunocompetent animals. As the resulting tumors initiated at highly defined locations, we could track their progression via fluorescence and documented deep invasion into tissues and metastatic deposits. TEAZ can be deployed to other tissues and cell types such as the heart with the use of suitable transgenic promoters. The versatility of TEAZ makes it widely accessible for rapid modeling of somatic gene alterations and cancer progression at a scale not achievable in other in vivo systems.

cancer biology↗