ABSTRACT Phylogenomics with dense taxon sampling offers a powerful means to resolve taxonomic and phylogenetic uncertainties. Hylodesmum is a legume genus with an East Asian (EA)–Eastern North American (ENA) disjunct distribution; however, its phylogeny and delimitation from Monarthrocarpus and Verdesmum remain uncertain. Here, we employed plastid genomes, nuclear ribosomal DNA, and 353 low‐copy nuclear genes to reconstruct the phylogeny of all recognized taxa across these genera. Our analyses consistently recover Verdesmum as nested within Hylodesmum, whereas Monarthrocarpus is distantly related. Within Hylodesmum, two major clades were recovered, which are better defined by flower color and leaf margin than by traditional morphological traits. Cytonuclear incongruence in the H. podocarpum and H. laxum complexes suggests likely chloroplast capture. Biogeographic reconstruction supports an “out of Himalaya‐Hengduan Mountains” origin for Hylodesmum, with a late Miocene dispersal to North America (ca. 7.35 Ma), followed by two back‐dispersals to Asia (ca. 5.67–4.98 Ma). This study reveals a complex history of bidirectional dispersal, likely facilitated by mammals, in an EA–ENA disjunct genus and provides a new phylogenetic framework for the taxonomic revision of Hylodesmum, recognizing 18 species within two sections.

Gynura Cassini (1825: 391) (Asteraceae: Senecioneae) is a medium-sized genus comprising approximately 45 species (Vanijajiva & Kadereit 2011; van der Ent & Vanijajiva 2014; Li et al. 2022; Calvo et al. 2025; Zhu et al. 2025a, 2025b). The genus is primarily distributed in tropical and subtropical regions of Asia and Africa, with Southeast Asia representing the major center of its diversity (Vanijajiva & Kadereit 2011). Morphologically, Gynura is characterized by homogamous discoid capitula and erect, exserted style branches with long, subulate appendages.

Gynura mollis, G. lyrata, and G. densiflora (Asteraceae: Senecioneae) were originally based on Zollinger’s collections from Java, Indonesia, but their identities have long been a source of confusion. In this study, we located their type material and clarify their identities. Our findings show that G. densiflora and G. mollis are conspecific with G. ajakensis, and G. mollis, with the priority, is revealed to be the correct name for this species. Gynura lyrata is conspecific with G. aurantiaca and is treated as a synonym of the latter. In addition, we clarified the cross-labelling issue among three Zollinger gatherings: HZ.442, HZ.606, and H.2592. The issue was caused by Zollinger’s specimen-numbering method and has led to significant nomenclatural and taxonomic confusions. This is also an important reminder to researchers working with Zollinger’s collections. Lastly, G. aurantiaca var. ovata is here synonymized with G. mollis, and lectotypes are designated for G. aurantiaca var. ovata, G. densiflora, and G. mollis.

The traditional Tree of Life (ToL) model is increasingly challenged by the Web of Life (WoL) paradigm, which offers a more accurate depiction of organismal phylogeny, particularly in light of the incongruences often observed between gene and species trees. However, the absence of a standardised method for resolving evolutionary mechanisms - such as Incomplete Lineage Sorting (ILS), hybridisation, introgression, polyploidisation, and whole-genome duplication - remains a significant obstacle in defining the WoL. Characterised by extensive hybridisation events, the pear genus Pyrus provides an ideal model for exploring these complexities. In this study, we present a Step-by-Step Exclusion (SSE) approach for investigating the evolutionary pathways of Pyrus, based on Whole Genome Sequencing (WGS) and Deep Genome Skimming (DGS) data, and our results demonstrate that: (1) ILS, rather than polyploidisation, plays a dominant role in the origination of Pyrus; (2) the two subgenera of Pyrus followed independent evolutionary paths, influenced by geographical barriers formed through the uplift of the Tibetan Plateau and increased aridity in Central Asia; (3) both ILS and hybridisation have driven the diversification of subg. Pashia, while hybridisation alone has shaped the reticulate evolution of subg. Pyrus; (4) the establishment of the Silk Road during the Han Dynasty facilitated genetic exchange between subg. Pyrus and subg. Pashia. The SSE approach offers a versatile framework for studying the evolutionary mechanisms underlying the WoL paradigm.

Anthocyanin, a water-soluble flavonoid pigment, serves as a key secondary metabolite and plays a major role in the formation of color in plant flowers, fruits and vegetables. Dihydroflavonol 4-reductase (DFR) is a key enzyme in the anthocyanin biosynthesis pathway, catalyzing the reduction of dihydroflavonols into leucoanthocyanidins. In this study, we presented the identification of a putative IlDFR gene from Iris lactea Pall var. chinensis. The amino acid sequences of IlDFR shares an evolutionary lineage among its same genus, and IlDFR showed high activity when dihydromyricetin (DHM) was used as a substrate, while less or no activity using dihydrokaempferol (DHK) or dihydroquercetin (DHQ) as a substrate in the enzymatic assay. This may be the reason way the I. lactea exhibits blue-purple color because it mainly biosynthesizes and accumulates delphinidins in its petals. The IlDFR expressed in a white flower variety of Petunia×hybrida converted noticeable different phenotypes that exhibited light to dark purple in their flowers. In a transgenic plant with dark purple flower and the highest expression level of IlDFR showed that the contents of delphinidin-based anthocyanins, including delphinidin and its methylated derivative petunidin, as well as their glycosides (glucoside, rutinoside, galactoside and sophoroside) were significantly in higher levels than those of no-transgenic negative control. These results further strengthened the evidence that IlDFR prefers DHM substrate. Our research will provide new gene resources and a basis for color modification of flowers, fruits and vegetables using molecular biology and genetic engineering techniques.

In contrast to the traditional Tree of Life (ToL) paradigm, the Web of Life (WoL) model provides a more nuanced and precise depiction of organismal phylogeny, particularly considering the prevalent incongruence observed among gene/species trees. The lack of a generalized pipeline for teasing apart potential evolutionary mechanisms-such as Incomplete Lineage Sorting (ILS), hybridization, introgression, polyploidization, and Whole-Genome Duplication-poses significant challenges to the delineation of the WoL. The pear genus Pyrus, characterized by extensive hybridization events, serves as an excellent model for investigating the WoL. This study introduces a novel Step-by-Step Exclusion (SSE) approach to deciphering the complexities inherent in the WoL. Our findings indicate: 1) ILS, rather than polyploidization, is identified as the primary driver behind the origin of Pyrus from the arid regions of the Himalayas-Central Asia; 2) the two subgenera of Pyrus have independent evolutionary trajectories, facilitated by the geographical barriers that arose via the uplift of the Tibetan Plateau and increased aridity in Central Asia; 3) ILS and hybridization have facilitated the diversification of Oriental pears, while hybridization alone has driven the reticulate evolution of Occidental pears; 4) the establishment of the Silk Road during the Han Dynasty acted as a conduit for genetic exchange between Occidental and Oriental pears. The novel SSE approach provides a universally applicable framework for investigating evolutionary mechanisms defining the WoL paradigm. ### Competing Interest Statement The authors have declared no competing interest.

The lack of a robust phylogenetic backbone has posed significant challenges to proposing an infrageneric taxonomic classification of the pear genus, Pyrus, a widely distributed Eurasian lineage of Rosaceae. This issue has been exacerbated by limited informative loci and inaccessible taxon sampling. To address these limitations, we conducted extensive taxon sampling, encompassing 78 Pyrus ingroup individuals representing 32 species, along with 4 outgroup species. This comprehensive sampling strategy covers a wide range of morphological and geographical variations. To enable accurate phylogenomic inference, we assembled 801 single-copy nuclear genes and 72 plastid coding sequences from deep genome skimming (DGS) data. Additionally, we employed a tree-based method for nuclear orthology inference, which led to the generation of three orthologous datasets: one-to-one orthologs (1to1), monophyletic outgroups (MO), and rooted ingroups (RT). The results yielded from both nuclear and plastid analyses consistently support the monophyly of Pyrus, and two well-supported clades, the Occidental and Oriental clades, were recovered in nine nuclear and three plastid trees. Integrating evidence from morphology and phylogenomics, we propose an updated infrageneric classification of Pyrus, which consists of two subgenera: P. subg. Pyrus and P. subg. Pashia stat. nov. This revised classification provides a more robust framework for understanding the evolutionary relationships within the pear genus.

Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex postpolyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works efficiently on genome-scale data and has high accuracy in identifying polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum pseudo-likelihood model of Phylonet, and genome-scale data, we further address the complex origin of Tussilagininae, a speciose group (ca. 45 genera and 710 species) characterized by having high base chromosome numbers (mainly x = 30, 40). In particular, the inferred patterns are strongly supported by the chromosomal evidence. Tussilagininae is revealed to comprise 2 large groups with successive allopolyploid origins: Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two allopolyploidy events first give rise to Tussilagininae s.s., with the first event occurring between the ancestor of subtribe Senecioninae (x = 10) and a lineage (highly probably with x = 10) related to the Brachyglottis alliance, and the resulting hybrid lineage crossing with the ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then, after early diversification, the Central American group (mainly x = 30) of Tussilagininae s.s., is involved in a third allopolyploidy event with, again, the Chersodoma lineage and produces the Gynoxyoid group. Our study highlights the value of HomeoSorter and the homeolog-sorting approach in polyploid phylogenetics. With rich species diversity and clear evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are also excellent models for future investigations of polyploidy.

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the sys-tematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/ or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Synotisjinpingensis (Asteraceae, Senecioneae), a new species from Jinping county in southeastern Yunnan province, China, is described and illustrated. This species is distinguished by having white ray florets in the genus Synotis, in which only species with yellow ray florets have been hitherto known. In habit and leaf shape S.jinpingensis is most closely similar to S.duclouxii, a species occurring in southwestern Guizhou, southern Sichuan and northeastern Yunnan, China, but differs, in addition to the color of ray florets, by having fewer lateral veins of leaves, obviously longer bracts of calyculus, and larger phyllaries. The membership of the new species within Synotis is strongly corroborated by evidence from floral micromorphology and phylogenetic analyses based on ITS sequence data. Color photographs of living plants, a distribution map, and provisional IUCN status of S.jinpingensis are provided.

Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa - A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.

Phylogenetic networks, rather than purely bifurcating trees, more accurately depict the intricate evolutionary dynamics of most lineages, especially those characterized by extensive hybridization and allopolyploidization events. However, the challenges of achieving complete taxon sampling, and limited financial resources for studying non-model plant lineages, have hindered comprehensive and robust estimation of phylogenetic backbones with guidance from networks. The bellflower tribe, Campanuleae, characterized by a reticulate evolutionary history, serves as an ideal model to investigate how to diagnose nested ancient reticulation events. Here, by integrating multiple genomic data sources and a range of phylogenetic inference methods, we produced a robust phylogenetic backbone for the tribe Campanuleae. Our investigation of reticulate evolution indicates that hybridization and allopolyploidization were instrumental in shaping the diversity of the bellflower tribe, particularly during the initial diversification of the subtribe Phytematinae. Additionally, we ascertained that conflicting topologies resulting from distinct genomic datasets and inference methodologies significantly impact downstream estimates of divergence dating, ancestral area construction, and diversification rates. This study offers a universally relevant framework for deciphering how to use network-based phylogenetic structures using various genomic sources and inference methods. [Campanulaceae, Campanuleae, Cytonuclear discordance, paralog, phylogenomics, reticulate evolution]

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic rela-tionships and estimate the historical biogeography of the apple genus Malus sensu lato, an econo-mically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phy-logeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis dem-onstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree dis-cordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our histor-ical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic dis-cordance and biogeographic analysis using deep genome skimming data sets.

Synotis nyalamensis (Asteraceae, Senecioneae), a new species from Nyalam county in southern Xizang (Tibet), China, is described and illustrated. It is most closely similar to S. kunthiana, a species occurring in northwestern India, Nepal, and Pakistan, in having abaxially white-tomentose leaves and cylindric-campanulate capitula, but differs by having higher stature (45–60 vs. 20–40 cm), singular (vs. several) stems, caudate-acuminate (vs. acuminate) leaf tips, prominent (vs. obscure) nerves on abaxial side of leaves, and more disk florets (15–24 vs. 7–12).

Arnica japonica L. f. and A. japonica Thunb. have long been controversial about their identities and nomenclature, largely due to the mysterious type material of Arnica japonica L. f. We locate the original material of Arnica japonica L. f., viz., LINN-HS 1322.1, and clarify the misleading description about its leaf form. Arnica japonica L. f. is revealed to be conspecific with A. japonica Thunb. Taxonomic and nomenclatural changes are made accordingly for these two names, and for Gynura japonica and Syneilesis palmata, another two names also involved in this issue. A second-step lectotype of Arnica japonica Thunb. is designated because of the taxonomically mixed material of the original lectotype.

The problems about the original material and typifications of Senecio plantaginifolius (= Ligularia virgaurea), S. setchuenensis (≡ Synotis setchuenensis), and S. souliei (≡ Parasenecio souliei) have been revisited. The correct lectotype of S. souliei is the P00705033 sheet of Soulié s.n. designated by Koyama (Acta Phytotax. Geobot. 30: 75. 1979), and that of S. plantaginifolius should be Soulié s.n. (P02676722) designated by Hu (Quart. J. Taiwan Mus. 21: 137. 1968). For S. setchuenensis, it is better to only accept the P00705011 and P00705012 sheets of Soulié 198 as its original material, and the lectotype is P00705011 designated by Yu et al. (Pl. Diversity Resources 36: 593. 2014).