Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae)

Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid-polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.

Deep reticulation: the long legacy of hybridization in vascular plant evolution

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.

Genomic evidence for homoploid hybrid speciation between ancestors of two different genera

Homoploid hybrid speciation (HHS) has been increasingly recognized as occurring widely during species diversification of both plants and animals. However, previous studies on HHS have mostly focused on closely-related species while it has been rarely reported or tested between ancestors of different genera. Here, we explore the likely HHS origin of Carpinus sect. Distegocarpus between sect. Carpinus and Ostrya in the family Betulaceae. We generate a chromosome-level reference genome for C. viminea of sect. Carpinus and re-sequence genomes of 44 individuals from the genera Carpinus and Ostrya. Our integrated analyses of all genomic data suggest that sect. Distegocarpus, which has three species, likely originates through HHS during the early divergence between Carpinus and Ostrya. Our study highlights the likelihood of an HHS event between ancestors of the extant genera during their initial divergences, which may have led to reticulate phylogenies at higher taxonomic levels.

Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) sensu lato (sl), comprising the platform, the Himalaya and the Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because of geographic isolation. However, gene flow has been widely detected during the speciation processes of all groups examined, suggesting that natural selection may have also played an important role during species divergence in this region. In addition, natural hybrids have been recovered in almost all species-rich genera. This suggests that numerous species in this region are still 'on the speciation pathway to complete reproductive isolation (RI)'. Such hybrids could directly develop into new species through hybrid polyploidization and homoploid hybrid speciation (HHS). HHS may take place more easily than previously thought through alternate inheritance of alleles of parents at multiple RI loci. Therefore, isolation, selection and hybridization could together have promoted species diversification of numerous plant genera on the QTP sl. We emphasize the need for identification and functional analysis of alleles of major genes for speciation, and especially encourage investigations of parallel adaptive divergence causing RI across different lineages within similar but specific habitats in this region.

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

The Eastern Asia (EA) - North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii-Thuja sutchuenensis and a "disjunct clade", where western NA species T. plicata is sister to an EA-eastern NA disjunct Thuja occidentalis-Thuja koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, approximately 20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.

Evolutionary origin of a tetraploid Allium species on the Qinghai-Tibet Plateau

Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2n = 4x = 32), one of the five known members in the subgenus Cyathophora. We found that A. tetraploideum was an obvious allotetrapoploid derived from ancestors including at least two closely related diploid species, A. farreri and A. cyathophorum, from which it differs by multiple ecological and genomic attributes. However, these two species cannot account for the full genome of A. tetraploideum, indicating that at least one extinct diploid is also involved in its ancestry. Furthermore, A. tetraploideum appears to have arisen via homoploid hybrid speciation (HHS) from two extinct allotetraploid parents, which derived in turn from the aforementioned diploids. Other modes of origin were possible, but all were even more complex and involved additional extinct ancestors. Our study together highlights how some polyploid species might have very complex origins, involving both HHS and polyploid speciation and also extinct ancestors.

Allopolyploid Speciation Accompanied by Gene Flow in a Tree Fern

Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid speciation as an evolutionary process in fern lineages remains poorly understood. Here, we employ flow cytometry, phylogeny, genomewide single nucleotide polymorphism data sets, and admixture and coalescent modeling to show that the scaly tree fern, Gymnosphaera metteniana is a naturally occurring allotetraploid species derived from hybridization between the diploids, G. denticulata and G. gigantea. Moreover, we detected ongoing gene flow between the hybrid species and its progenitors, and we found that G. gigantea and G. metteniana inhabit distinct niches, whereas climatic niches of G. denticulata and G. metteniana largely overlap. Taken together, these results suggest that either some degree of intrinsic genetic isolation between the hybrid species and its parental progenitors or ecological isolation over short distances may be playing an important role in the evolution of reproductive barriers. Historical climate change may have facilitated the origin of G. metteniana, with the timing of hybridization coinciding with a period of intensification of the East Asian monsoon during the Pliocene and Pleistocene periods in southern China. Our study of allotetraploid G. metteniana represents the first genomic-level documentation of hybrid speciation in scaly tree ferns and, thus, provides a new perspective on evolution in the lineage.

Perspectives on the clonal persistence of presumed 'ghost' genomes in unisexual or allopolyploid taxa arising via hybridization

Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as ‘ghost species’ after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.

An extinct vertebrate preserved by its living hybridogenetic descendant

Hybridogenesis is a special mode of hybrid reproduction where one parental genome is eliminated and the other is transmitted clonally. We propose that this mechanism can perpetuate the genome of extinct species, based on new genetic data from Pelophylax water frogs. We characterized the genetic makeup of Italian hybridogenetic hybrids (P. kl. hispanicus and esculentus) and identified a new endemic lineage of Eastern-Mediterranean origin as one parental ancestor of P. kl. hispanicus. This taxon is nowadays extinct in the wild but its germline subsists through its hybridogenetic descendant, which can thus be considered as a "semi living fossil". Such rare situation calls for realistic efforts of de-extinction through selective breeding without genetic engineering, and fuels the topical controversy of reviving long extinct species. "Ghost" species hidden by taxa of hybrid origin may be more frequent than suspected in vertebrate groups that experienced a strong history of hybridization and semi-sexual reproduction.