Homoploid Hybrid Research Articles

Genomic changes and stabilization following homoploid hybrid speciation of the Oxford ragwort Senecio squalidus

Oxford ragwort (Senecio squalidus) is one of only two homoploid hybrid species known to have originated very recently, so it is a unique model for determining genomic changes and stabilization following homoploid hybrid speciation. Here, we provide a chromosome-level genome assembly of S.squalidus with 95% of the assembly contained in the 10 longest scaffolds, corresponding to its haploid chromosome number. We annotated30,249 protein-coding genes and estimated that ∼62% of the genome consists of repetitive elements. We then characterized genome-wide patterns of linkage disequilibrium, polymorphism, and divergence in S.squalidus and its two parental species, finding that (1) linkage disequilibrium is highly heterogeneous, with a region on chromosome 4 showing increased values across all three species but especially in S.squalidus; (2) regions harboring genetic incompatibilities between the two parental species tend to be large, show reduced recombination, and have lower polymorphism in S.squalidus; (3) the two parental species have an unequal contribution (70:30) to the genome of S.squalidus, with long blocks of parent-specific ancestry supporting a very rapid stabilization of the hybrid lineage after hybrid formation; and (4) genomic regions with major parent ancestry exhibit an overrepresentation of loci with evidence for divergent selection occurring between the two parental species on Mount Etna. Our results show that both genetic incompatibilities and natural selection play a role in determining genome-wide reorganization following hybrid speciation and that patterns associated with homoploid hybrid speciation-typically seen in much older systems-can evolve very quickly following hybridization.

Phylogeographic analysis reveals multiple origins of the desert shrub Reaumuria songarica in northern Xinjiang, involving homoploid and tetraploid hybrids.

Hybrid speciation plays an important role in species diversification. The establishment of reproductive isolation is crucial for hybrid speciation, and the identification of diverse types of hybrids, particularly homoploid hybrid species, contributes to a comprehensive understanding of this process. Reaumuria songarica is a constructive shrub widespread in arid Central Asia. Previous studies have inferred that the R. songarica populations in the Gurbantunggut Desert (GuD) originated from homoploid hybridizations between its eastern and western lineages and may have evolved into an incipient species. To further elucidate the genetic composition of different hybrid populations and to determine the species boundary of this hybrid lineage, we investigated the overall phylogeographic structure of R. songarica based on variation patterns of five cpDNA and one nrITS sequences across 32 populations. Phylogenetic analyses demonstrated that within the GuD lineage, the Wuerhe population evolved directly from ancestral lineages, whereas the others originated from hybridizations between the eastern and western lineages. PCoA and genetic barrier analysis supported the subdivision of the GuD lineage into the southern (GuD-S) and northern (GuD-N) groups. Populations in the GuD-S group had a consistent genetic composition and the same ancestral female parent, indicating that they belonged to a homoploid hybrid lineage. However, the GuD-N group experienced genetic admixture of the eastern and western lineages on nrITS and cpDNA, with some populations inferred to be allopolyploid based on ploidy data. Based on cpDNA haplotypes, BEAST analyses showed that the GuD-S and GuD-N groups originated after 0.5 Ma. Our results suggest that multiple expansions and contractions of GuD, driven by Quaternary climatic oscillations and the Kunlun-Yellow River tectonic movement, are important causes of the complex origins of R. songarica populations in northern Xinjiang. This study highlights the complex origins of the Junggar Basin flora and the underappreciated role of hybridization in increasing its species diversity.

A morphological study on the question of the hybrid origin of Astrophytum coahuilense (Cactaceae)

Two alternative hypotheses may explain the origin of Astrophytum coahuilense. One hypothesis is that A. coahuilense is an ancient diploid hybrid derived from interbreeding between A. capricorne and A. myriostigma. An alternative is that A. coahuilense arose via allopatric speciation and its similarity to A. myriostigma in vegetative characters is due to convergent evolution. The two hypotheses are tested, applying univariate analysis and Non-metric Multidimensional Scaling analysis to morphological datasets. Univariate analysis, which is based on 13 vegetative and 10 reproductive characters, shows that the morphology of A. coahuilense is complex, consisting of a combination of vegetative and reproductive characters shared with both A. capricorne and A. myriostigma as well as several intermediate traits. Furthermore, the morphology of A. coahuilense lacks unique, fixed characteristics. Non-metric Multidimensional Scaling analysis of 15 characters (three vegetative and 12 reproductive traits) produced a two-dimensional scatterplot in which the cluster representing A. coahuilense occupies a position intermediate between the clusters of the two parental species along Dimension 1. Thus, both analyses support the hypothesis that Astrophytum coahuilense originated through hybridization between A. capricorne and A. myriostigma. Biological and ecological factors that may have facilitated homoploid hybrid speciation are discussed.

Documenting homoploid hybrid speciation.

Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo-species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that - given the ubiquity of admixture and the polygenic basis of reproductive isolation - homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies.

Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers.

The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non-model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.

Hybrid speciation driven by multilocus introgression of ecological traits

Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species1,2. However, convincing examples of homoploid hybrid speciation remain rare because it is challenging to demonstrate that hybridization was crucial in generating reproductive isolation3. Here we combine population genomic analysis with quantitative trait locus mapping of species-specific traits to examine a case of hybrid speciation in Heliconius butterflies. We show that Heliconius elevatus is a hybrid species that is sympatric with both parents and has persisted as an independently evolving lineage for at least 180,000 years. This is despite pervasive and ongoing gene flow with one parent, Heliconius pardalinus, which homogenizes 99% of their genomes. The remaining 1% introgressed from the other parent, Heliconius melpomene, and is scattered widely across the H. elevatus genome in islands of divergence from H. pardalinus. These islands contain multiple traits that are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones and mate choice. Collectively, these traits place H. elevatus on its own adaptive peak and permit coexistence with both parents. Our results show that speciation was driven by introgression of ecological traits, and that speciation with gene flow is possible with a multilocus genetic architecture.

Altai Mountains – cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)

AbstractMountains form a diverse mosaic of microhabitats over small distances created by changes in climate, soil, and water availability. A key to adaptation of plants to such microhabitats is genetic variation; however, natural accumulation of genetic variation through mutation is slow and often not sufficient alone. Adaptive introgression via hybridization is an alternative to generate genetic variation. Here, we investigate hybridization and discuss its adaptive role in Veronica subg. Pseudolysimachium at their Altai Mountains distribution. To support our hypotheses of frequent hybridization, we genotyped thousands of SNPs for 233 individuals from 10 species and 7 putative hybrids previously described based on morphology. We employed Bayesian and likelihood statistical models and supported our results by morphometric analysis and genomic in situ hybridization (GISH). The results suggest that almost all the individuals of the putative hybrids are of F1 type. The GISH investigation in one case strongly supports homoploid hybridization (origin of V. ×schmakovii from V. longifolia and V. porphyriana. Divergence times of Altai Veronica species are estimated to be within 1–2 million years ago with high probability of gene flow over that time. Our results also demonstrate that the direction of gene flow is mainly from the locally endemic V. porphyriana. We hypothesize that the large Siberian plains and topographically diverse foreland of the Altai Mountains provide an ideal setting for hybridization with the potential for adaptive introgression of alleles conferring tolerance to cooler climates, to the lowland species migrating into the Altai Mountains.

Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong.

Butylphthalide is one of the first-line drugs for ischemic stroke therapy, while no biosynthetic enzyme for butylphthalide has been reported. Here, we present a haplotype-resolved genome of Ligusticum chuanxiong, a long-cultivated and phthalide-rich medicinal plant in Apiaceae. On the basis of comprehensive screening, four Fe(II)- and 2-oxoglutarate-dependent dioxygenases and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturases (P4,5Ds) that effectively promoted the forming of (S)-3-n-butylphthalide and butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity in L. chuanxiong. Notably, comparative genomic evidence supported L. chuanxiong as a homoploid hybrid with Ligusticum sinense as a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago. Our study is an icebreaker for the dissection of phthalide biosynthetic pathway and reveals the hybrid origin of L. chuanxiong, which will facilitate the metabolic engineering for (S)-3-n-butylphthalide production and breeding for L. chuanxiong.

Hedysarumqilianshanense sp. nov. (Fabaceae, Hedysareae), a new species from the Qilianshan Mountains in Gansu, China.

Hedysarumqilianshanensesp. nov. (Fabaceae, Hedysareae) is described and illustrated from the Qilianshan Mountains in Gansu, China. This new species is similar to H.przewalskii, but can be distinguished by its corolla being light purple to purple, standard 15-19 mm long, wings 14-16 mm long, keels 16-19 mm long, and the ovary and legume being glabrous. The new species can be easily distinguished from H.neglectum Ledeb. by its bract being shorter than the pedicel, and the ovary and legume being glabrous. Phylogenetic tree based on the nuclear ITS and ETS sequences shows that H.qilianshanense is sister to H.przewalskii, while the tree based on the plastid psbA-trnH, trnC-petN, trnL-F, trnS-G and petN-psbM sequences shows H.qilianshanense as sister to a clade consisting of H.hedysaroides, H.inundatum, H.americanum and H.neglectum. The new species is a diploid with the chromosome number 2n = 14. Based on morphological, phylogenetic and karyotypic evidence, the new species may originate from an ancient homoploid hybrid speciation event.

Israeli Oncocyclus irises: Phylogenetic relationships and evolutionary history

Abstract Oncocyclus is a large group of bearded irises with poorly known phylogeny and evolutionary history. In Israel, Iris sect. Oncocyclus comprises eight species belonging to three aggregates. We used a combination of approaches to resolve the phylogenetic relationships of these species and indicate the evolutionary forces responsible for their origin. We sequenced the whole chloroplast genomes of species and integrated a phylogenetic tree with results of genetic (AFLP) divergence, degree of reproductive isolation, and species distribution modeling. Our findings suggest that quantitative and even qualitative morphological characters, such as flower color, are unreliable diagnostic traits for Oncocyclus taxonomy; that some recognized species comprise more than one species; and that group evolution did not involve the origin of distinct flower aggregates. A lack of pre-zygotic reproductive isolation agrees with the very low variability of the Oncocyclus plastome, suggesting that Israeli Oncocyclus species are very young. Homoploid hybridization followed or preceded by long periods of geographic isolation, and local selection likely contributed to speciation in Oncocyclus. In the group evolutionary history, importance of homoploid hybridization and local selection differed among species, but limited gene flow played a crucial role for all species.

Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum.

Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.

In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation?

Hybridization opens a unique window for observing speciation mechanisms and is a potential engine of speciation. One controversially discussed outcome of hybridization is homoploid hybrid speciation by reciprocal sorting, where a hybrid population maintains a mixed combination of the parental genetic incompatibilities, preventing further gene exchange between the newly formed population and the two parental sources. Previous work showed that, for specific linkage architectures (i.e., the genomic location and order of hybrid incompatibilities), reciprocal sorting could reliably result in hybrid speciation. Yet, the sorting of incompatibilities creates a risk of population extinction. To understand how the demographic consequences of the purging of incompatibilities interact with the formation of a hybrid species, we model an isolated hybrid population resulting from a single admixture event. We study how population size, linkage architecture, and the strength of the incompatibility affect survival of the hybrid population, resolution/purging of the genetic incompatibilities and the probability of observing hybrid speciation. We demonstrate that the extinction risk is highest for intermediately strong hybrid incompatibilities. In addition, the linkage architecture displaying the highest hybrid speciation probabilities changes drastically with population size. Overall, this indicates that population dynamics can strongly affect the outcome of hybridization and the hybrid speciation probability.

Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation.

Despite the importance of hybridization in evolution, the evolutionary consequence of homoploid hybridizations in plants remains poorly understood. Specially, homoploid hybridization events have been rarely documented due to a lack of genomic resources and methodological limitations. Actinidia zhejiangensis was suspected to have arisen from hybridization of Actinidia eriantha and Actinidia hemsleyana or Actinidia rufa. However, this species was very rare in nature and exhibited sympatric distribution with its potential parent species, which implied it might be a spontaneous hybrid of ongoing homoploid hybridization. Here, we illustrate the dead-end homoploid hybridization and genomic basis of isolating barriers between A. eriantha and A. hemsleyana through whole genome sequencing and population genomic analyses. Chromosome-scale genome assemblies of A. zhejiangensis and A. hemsleyana were generated. The chromosomes of A.zhejiangensis are confidently assigned to the two haplomes, and one of them originates from A. eriantha and the other originates from A. hemsleyana. Whole genome resequencing data reveal that A. zhejiangensis are mainly F1 hybrids of A. hemsleyana and A. eriantha and gene flow initiated about 0.98 million years ago, implying both strong genetic barriers and ongoing hybridization between these two deeply divergent kiwifruit species. Five inversions containing genes involved in pollen germination and pollen tube growth might account for the fertility breakdown of hybrids between A. hemsleyana and A. eriantha. Despite its distinct morphological traits and long recurrent hybrid origination, A. zhejiangensis does not initiate speciation. Collectively, our study provides new insights into homoploid hybridization in plants and provides genomic resources for evolutionary and functional genomic studies of kiwifruit.

Backcrossing to different parents produced two distinct hybrid species.

Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in the conifer Picea brachytyla. Our analyses revealed non-sister relationships for two lineages of P. brachytyla, with the southern lineage being placed within the re-circumscribed P. likiangensis species complex (PLSC) and P. brachytyla sensu stricto (s.s.) consisted solely of the northern lineage, forming a distinct clade that is paratactic to both the PLSC and P. wilsonii. Our phylogenetic and coalescent analyses suggested that P. brachytyla s.s. arose from HHS between the ancestor of the PLSC before its diversification and P. wilsonii through an intermediate hybrid lineage at an early stage and backcrossing to the ancestral PLSC. Additionally, P. purpurea shares the same parents and an extinct lineage with P. brachytyla s.s. but backcrossing to the other parent, P. wilsonii at a later stage. We reveal the first case that backcrossing to different parents of the same extinct hybrid lineage produced two different hybrid species. Our results highlight the existence of more reticulate evolution during species diversification in the spruce genus and more complex homoploid hybrid events than previously identified.

Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator

Hybridization is widespread and constitutes an important source of genetic variability and evolution. In animals, its role in generating novel and independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis is a marine apex predator of Pacific and Atlantic waters, with a disjunct set of populations in Peru and Northern Chile [Peruvian fur seal (Pfs)] with controversial taxonomic status. We demonstrate, using complete genome and reduced representation sequencing, that the Pfs is a genetically distinct species with an admixed genome that originated from hybridization between the SAfs and the Galapagos fur seal (Arctocephalus galapagoensis) ~400,000 years ago. Our results strongly support the origin of Pfs by homoploid hybrid speciation over alternative introgression scenarios. This study highlights the role of hybridization in promoting species-level biodiversity in large vertebrates.

Evolution of South African brambles (Rubus L.) – new insights from molecular markers

Background: South African brambles (Rubus L., Rosaceae) represent a complex group of six native species and at least 12 introduced taxa with different ploidy levels and varying tendencies to hybridisation. The role of hybridisation, introgression and apomixis in the ongoing evolution has been hypothesised based on morphological observations, but it has not been rigorously studied to date, and nor has the phylogeny of the group. Objectives and methods: This paper aims to reveal the evolutionary patterns and mechanisms in South African brambles by employing three types of molecular markers: plastid and nuclear ribosomal DNA sequences, and nuclear microsatellites. Results: The data confirmed the tetraploid R. thaumasius A.Beek and diploid R. ludwigii Eckl. & Zeyh. as distinct native species, while the other four native species are shown to be closely related and likely derived from three ancestors. Conclusion: Ancient hybridisation and limited gene flow between regions (particularly between winter- and summer-rainfall zones) appear to be the main drivers of current patterns in the tetraploid R. pinnatus Willd. and hexaploid R. rigidus Sm. Current hybridisation is also likely, although rare. The mechanism of ‘octoploid bridge’ is proposed, which overcomes the ploidy reproduction barrier between R. pinnatus (or other tetraploids) and R. rigidus. No gene flow was detected between native and alien taxa, but clonal duplications were discovered in the R. bergii × pinnatus hybrid, which implies the possibility of apomictic spread of homoploid hybrids formed between native and introduced brambles and the potential for a new invasion. On the other hand, heteroploid hybrids (R. bergii × rigidus) are formed recurrently and spread only vegetatively.

Effects of Microbial Communities on Elevational Gradient Adaptation Strategies of Pinus yunnanensis Franch. and Pinus densata Mast. in a Mixed Zone

Pinus densata Mast. is considered a homoploid hybrid species that originated from the putative parent species Pinus tabuliformis Carr. and Pinus yunnanensis Franch., but the mechanism of the adaptive differentiation of P. densata and its parents in native habitats has not been reported. Therefore, the overlapping distribution areas between P. densata and P. yunnanensis in the heart of the Hengduan Mountains were chosen. The adaptive differentiation mechanism of the homoploid hybrids and their parents with respect to the elevational gradient was studied based on the morphological features and the different strategies of recruiting endophytic microbial communities from the rhizosphere soil. The results showed that (1) the height and diameter at breast height were the greatest at 2600 m and 2900 m, and from 2700 m to 2900 m, three-needle pines (P. yunnanensis-like type) transitioned into two-needle pines (P. densata-like type). (2) The recruitment of rhizosphere microbial communities was driven by the C, N, P and pH values which showed significant elevation features. (3) There was a significant difference in the recruitment strategies of endophytes between the P. yunnanensis-like type and P. densata-like type. Pinus densata mainly reduced the recruitment of Mucoromycota (fungi) and increased the recruitment of Proteobacteria (bacteria), which may be related to environmental adaptability, quorum sensing and the metabolism of auxiliary factors and vitamins at high elevations. (4) The root endophytic microbiome was enriched in the rare groups from the rhizosphere soil microbial pool. The results of this study provide new insights and new ideas for environmental adaptability and differentiation in homoploid hybrid speciation.

Forest health in the Anthropocene: the emergence of a novel tree disease is associated with poplar cultivation.

Plant domestication and movement are large contributors to the success of new diseases. The introduction of new host species can result in accelerated evolutionary changes in pathogens, affecting long-established coevolutionary dynamics. This has been observed in poplars where severe epidemics of pathogens that were innocuous in their natural pathosystems occurred following host domestication. The North American fungus Sphaerulina musiva is responsible for endemic leaf spots on Populus deltoides. We show that the expansion of poplar cultivation resulted in the emergence of a new lineage of this pathogen that causes stem infections on a new host, P. balsamifera. This suggests a host shift since this is not a known host. Genome analysis of this emerging lineage reveals a mosaic pattern with islands of diversity separated by fixed genome regions, which is consistent with a homoploid hybridization event between two individuals that produced a hybrid swarm. Genome regions of extreme divergence and low diversity are enriched in genes involved in host-pathogen interactions. The specialization of this emerging lineage to a new host and its clonal propagation represents a serious threat to poplars and could affect both natural and planted forests. This work provides a clear example of the changes created by the intensification of tree cultivation that facilitate the emergence of specialized pathogens, jeopardizing the natural equilibrium between hosts and pathogens. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Recent natural hybridization inElymusandCampeiostachysof Triticeae: evidence from morphological, cytological and molecular analyses

AbstractNatural hybrids in Triticeae have been frequently reported from the Qinghai–Tibet plateau, but minor variation in morphological features and homoploid hybridization have made it difficult to identify the origin and genome constitution of hybrids between Elymus and Campeiostachys. Specimens were investigated using morphology, cytogenetics and phylogenetic analyses to uncover the genome constitution and origin of ten putative natural hybrids (SH01-SH10) from the Qinghai–Tibet plateau. SH01, SH02, SH03, SH05 and SH06 (2n = 5x = 35, StStHHY) originated from Campeiostachys breviaristata (2n = 6x = 42, StStHHYY) and Elymus sibiricus (2n = 4x = 28, StStHH); SH04 and SH07 (2n = 5x = 35, StStHHY) originated from C. nutans (2n = 6x = 42, StStHHYY) and E. sibiricus; SH08 (2n = 5x = 35, StStHHY) originated from C. dahurica var. tangutorum (2n = 6x = 42, StStHHYY) and E. sibiricus; and SH09 and SH10 (2n = 4x = 28, StStHH) were the homoploid hybrids of E. sibiricus and an unknown Elymus sp. (2n = 4x = 28, StStHH). Karyotype variations in SH04 and SH07 might originate from the maternal progenitor. Frequent hybridization in the Qinghai–Tibet plateau might result from factors such as genome constitution, pollination habits, overlapping flowering stage, sympatric distribution and unique ecological conditions.

Re-evaluating Homoploid Reticulate Evolution in Helianthus Sunflowers.

Sunflowers of the genus Helianthus are models for hybridization research and contain three of the best-studied examples of homoploid hybrid speciation. To understand a broader picture of hybridization within the annual sunflowers, we used whole-genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with increasing recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore, H. anomalus and H. deserticola appear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. This means our results are consistent with, but not definitive proof of, two ancient independent homoploid hybrid speciation events in the genus. Using a broader data set that covers the whole Helianthus genus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus, Helianthus can be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.