Hybridization Events Research Articles

Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia

AbstractAimPinaceae have been noted for their tendency towards reticulation as a result of interspecific hybridization. Here, we demonstrated the phylogeographic dynamics of the native Northeast Asian sub‐alpine conifer, Abies nephrolepis species complex (ANSC), evolving in circular overlaps along the Northeast Asian landform, which functions as a corridor with the sea, thus acting as a geographic barrier.LocationNortheast Asia: the Korean Peninsula, Japanese Archipelago, Russian Far East and northeastern China.TaxonAbies nephrolepis species complex (Family Pinaceae, Genus Abies, Section Balsamea, Abies nephrolepis, A. koreana, A. veitchii and A. sachalinensis).MethodsA total of 728 individuals from 38 ANSC populations were analysed using multiplexed inter‐simple sequence repeat genotyping by sequencing to capture variations in biparental nuclear genomes. Eight mitochondrial regions and eight chloroplast regions of each individual were sequenced using the MiSeq platform and Sanger sequencing. Species distribution models were generated.ResultsBayesian clustering with 507 nuclear single nucleotide polymorphisms and the discrepancy between cytoplasmic and nuclear genome lineages implied contemporary and ancient connections between neighbouring species in the form of circular overlap. This genetic connectivity was supported by principal component analysis. Strong correlations between genetic distance and geographic distance were observed, suggesting that gene flow occurs through a continuous chain around the sea. We also found that gene flow direction and intensity changed over time, with support from palaeodistribution modelling.ConclusionPast hybridization events were captured in cytoplasmic genomes, generating heterogeneity across maternal ancestries. This intensive phylogeographic study demonstrates speciation with incomplete reproductive isolation (continuous gene flow) among neighbouring species with an alteration of the direction and intensity of gene flow due to climate change. The divergence of ANSC due to repeated isolation and reconnection caused by heterogenous physiological environments and climate fluctuation provides a model to solve evolutionary scenarios for reticulate evolution in Pinaceae and other plants.

Serious Games for Seismic Risk Education: The Case of the ENP-CP Project

This paper delves into the potential advantages of integrating gamification into seismic risk management education, with a specific emphasis on the efficacy of serious games in augmenting the learning process. It offers an illustration of gamification within the framework of a seismic risk preparedness project involving multiple countries, languages, and cultures and across the time of the COVID-19 pandemic. The innovation of this approach largely lies in shifting the focus from competition, which is typical in most games, to collaboration. Three digital serious games were implemented to tackle facets of seismic risk management that are particularly favourable for empowering communities at risk. These games were first used in a hybrid event where students from Algeria, Morocco, and Italy engaged in gameplay both in person within their respective classrooms and remotely with classes in each country. The evaluation study showed the positive impact of gamification in captivating young participants and thereby instilling best practices in seismic risk management.

We know very little about pollination in the Platanthera Rich (Orchidaceae: Orchidoideae).

The Platanthera Rich. (Orchidoideae) comprise a speciose genus of orchids primarily in the northern hemisphere, with up to 200 known species worldwide. Individual species are known to self-pollinate, but many rely on insect pollinators with characteristics such as floral color, timing of floral odor emissions, nectar rewards, and spur length associated with particular pollination syndromes. As with many orchids, some orchid-pollinator associations are likely highly co-evolved, but we also know that some Platanthera spp. are the result of hybridization events, which implies a lack of pollinator fidelity in some cases. Some Platanthera spp. occur in large numbers which, coupled with the numerous Platanthera-pollinator systems, make them accessible as study species and useful for co-evolutionary studies. Due to the likely effects of climate change and ongoing development on Platanthera spp. habitats, these orchids and their associated pollinators should be a focus of conservation attention and management. However, while there is a fairly substantial literature coverage of Platanthera-pollinator occurrence and interactions, there are still wide gaps in our understanding of the species involved in these systems. In this systematic review, we outline what is current knowledge and provide guidance on further research that will increase our understanding of orchid-insect co-evolutionary relationships. Our review covers 157 orchid species and about 233 pollinator species interacting with 30 Platanthera spp. We provide analyses on aspects of these interactions such as flower morphology, known insect partners of Platanthera species, insect-Platanthera specificity, pollination visitor timing (diurnal vs. nocturnal), floral rewards, and insect behavior affecting pollination outcomes (e.g., pollinia placement). A substantial number of Platanthera spp. and at least a few of their known pollinators are of official (IUCN) conservation concern - and many of their pollinators remain unassessed or even currently unknown - which adds to the urgency of further research on these co-evolved relationships.

Simulating a hybridization event of a range-expanding sexual cannibal (Argiope bruennichi)

Abstract Hybridization plays an important role in animal speciation. Mediterranean populations of the Palaearctic wasp spider Argiope bruennichi have recently undergone a range expansion northwards. Adaptation to colder winters was facilitated by introgressed alleles derived from Asian populations, hence the resulting hybrids were able to expand geographically. Argiope bruennichi exhibits a highly complex mating system that includes strong sexual conflict and predisposes the species to behaviours that could facilitate directed hybridization and hybrid stabilization. To test this, we simulated a hybridization event with European and Asian spiders and a backcrossing event with southern and northern European spiders by conducting mate choice experiments and mating trials. We found pronounced differences in the cannibalism and monopolization successes between the populations. Asian male spiders were more successful in monopolizing European females than their European conspecifics and more successful than European males with Asian females. This would have led to an increased proportion of these specific offspring in the hybrid population. Our results suggest the mating system as a driving factor in the directional hybridization of Asian males and European females and the establishment of new northern European populations of A. bruennichi. We found no influences of the mating system on the stabilization of the resulting hybrid populations, probably owing to cold survival adaptations being a more important factor.

Critical Issues on the Surface Functionalization of Plasmonic Au-Ag/TiO2 Thin Films with Thiolated Oligonucleotide-Based Biorecognition Elements

This work reports on the surface functionalization of a nanomaterial supporting localized surface plasmon resonances (LSPRs) with (synthetic) thiolated oligonucleotide-based biorecognition elements, envisaging the development of selective LSPR-based DNA biosensors. The LSPR thin-film transducers are composed of noble metal nanoparticles (NPs) embedded in a TiO2 dielectric matrix, produced cost-effectively and sustainably by magnetron sputtering. The study focused on the immobilization kinetics of thiolated oligonucleotide probes as biorecognition elements, followed by the evaluation of hybridization events with the target probe. The interaction between the thiolated oligonucleotide probe and the transducer’s surface was assessed by monitoring the LSPR signal with successive additions of probe solution through a microfluidic device. The device was specifically designed and fabricated for this work and adapted to a high-resolution LSPR spectroscopy system with portable characteristics. Benefiting from the synergetic characteristics of Ag and Au in the form of bimetallic nanoparticles, the Au-Ag/TiO2 thin film proved to be more sensitive to thiolated oligonucleotide binding events. Despite the successful surface functionalization with the biorecognition element, the detection of complementary oligonucleotides revealed electrostatic repulsion and steric hindrance, which hindered hybridization with the target oligonucleotide. This study points to an effect that is still poorly described in the literature and affects the design of LSPR biosensors based on nanoplasmonic thin films.

The spatial ecology of Mojave rattlesnakes (Crotalus scutulatus), prairie rattlesnakes (Crotalus viridis), and their hybrids in southwestern New Mexico

Abstract Hybridization between species provides unique opportunities to understand evolutionary processes that are linked to reproductive isolation and, ultimately, speciation. However, the extrinsic factors that limit hybridization are poorly understood for most animal systems. Although the spatial ecology of individuals in natural habitats is fundamental to shaping reproductive success and survival, analyses of the spatial ecology of hybrids and their parental groups are rarely reported. Here, we used radiotelemetry to monitor wild rattlesnakes across an interspecific hybrid zone (Crotalus scutulatus and Crotalus viridis) and measured movement parameters and space use (utilization distributions) of individuals to evaluate the hypothesis that hybridization resulted in transgressive or atypical movement patterns. Unexpectedly, of the spatial metrics we investigated, we found that hybrids were very similar to parental individuals. Nonetheless, hybrids did show increased patchiness of core utilization distributions, but this result is likely to be driven by increased habitat patchiness in the hybrid zone. Overall, we did not find evidence for overt extrinsic barriers to hybridization associated with spatial ecology; thus, we suggest that the close evolutionary history between the two parental species and their ecological and behavioural similarities are likely to increase the probability of hybridization events in this unique region of New Mexico.

Sedimentary characteristics of mixed source fine-grained gravity-flow and its significance for shale oil exploration in a lacustrine depression basin: A case study of the Chang 73 Sub-member of the Triassic Yanchang Formation in Ordos Basin, NW China

This study investigates the transport and evolution of fine-grained gravity-flow deposits in lacustrine basins, focusing on the relationship between fine-grained deposits and their respective source–reservoir combinations. Such knowledge is vital for the exploration and development of unconventional oil and gas resources within the source-rock series of continental lake basins in China. We investigated the fine-grained gravity-flow deposits of the Late Triassic Chang73 Sub-member within the Yanchang Formation in the Ordos Basin. Our approach combined core observations, field outcrop evaluations, thin section analysis, scanning electron microscopy, geochemical data, and laboratory measurements. The sedimentary facies, characteristics, controlling factors, and sedimentary model of the fine-grained gravity-flow deposits are investigated. The primary sources of fine-grained sediments are terrestrial clastic and volcanic–hydrothermal fine-grained sediments. These sediments are mainly developed in warm, humid environments with abundant precipitation, favoring a highly reducible hypoxic terrestrial brackish–freshwater environment. Ten lithofacies and eight bed types of fine-grained gravity-flow deposits are categorized. Bed types represent deposits of muddy slide deposits, muddy slump deposits, muddy debris flow deposits, muddy flow deposits, hybrid event beds, fine-grained transitional flow deposits, surge-like turbidity flow deposits, and fine-grained hyperpycnal flow deposits. As a result of paleo-seismicity, volcanic events, and paleogeomorphology, instability and subsequent collapse of the delta front sediments led to the formation of gravity-flow deposits. These deposits formed the “channel–lobe complex” and “sublacustrine fan” sedimentary systems in both the southwestern and northeastern parts of the basin, respectively. Meanwhile, extraordinary flood events formed during the Carnian Pluvial Episode (CPE) played a significant role. It prompted increased fluvial drainage that drove fine-grained hyperpycnal flows through pre-existing valley systems, resulting in the establishment of the “channel–lobe complex” sedimentary system. The Chang 73 Sub-member contains high-quality hydrocarbon source rocks, laying the foundation for shale oil. The introduction of volcanic ash and the influence of hydrothermal activities amplify the enrichment of organic matter within the lacustrine basin. Fine-grained gravity-flow deposits yield siltstone-rich sweet intervals, primarily seen in surge-like turbidity and hyperpycnal flows. The interbedding of sandy and muddy sediments, influenced by hybrid event beds and fine-grained transitional flows, establishes a stratigraphic arrangement in which the upper layer nourishes the underlying reservoir. This structure is particularly beneficial for the development of shale oil and gas sweet intervals.

Ancient and recent origins of shared polymorphisms in yeast.

Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.

Incomplete lineage sorting and gene flow within Allium (Amayllidaceae)

The phylogeny and systematics of the genus Allium have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make Allium a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 Allium species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus Allium. We presented clear evidence for substantial ILS across the phylogeny of Allium. Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. Butomissa as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of Allium. This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled Allium species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.

Preface

The 2023 3rd International Conference on Measurement Control and Instrumentation (MCAI 2023) was grandly held in Guangzhou, China from November 24th to 26th, 2023 (hybrid event). Scholars, experts and enterprise representatives from all over the world gathered together to discuss the latest research results, technological advances and innovative applications in the field of measurement control and instrumentation.This Conference was organized in a variety of formats, including keynote speeches, oral presentations, poster presentations, Q&A sessions, academic investigation, etc., aiming to provide a platform for participants to present their achievements, have in-depth exchanges, and discuss collaborations. Over 300 representatives attended the conference, including experts with outstanding achievements in the field of measurement control and instrumentation as well as young researchers and graduate students interested in the field. They are actively committed to advancing the field and promoting academic exchanges and collaborations through this international conference. Participants listened to the presentations of outstanding researchers from all over the world and engaged in in-depth discussions and exchanges with them.The Proceedings of MCAI 2023 contains top academic papers from all over the world, which cover a wide range of topics and cutting-edge researches in the field of measurement control and instrumentation, including but not limited to: Numerical Control Technology, Precision Assessment, Microsensor Technology and Applications, Intelligent Instruments and Machinery, etc. The Editorial Board, a group of experts with rich experience and outstanding achievements in related fields, were responsible for reviewing and selecting the best papers to ensure the high quality and academic impact of the Proceedings.By sharing the latest research results and technology applications, we are confident that MCAI 2023’s Proceedings will be an important literature resource in the field of measurement control and instrumentation, providing researchers with an extensive knowledge base that will help them keep abreast of the latest research development and technology trends.Finally, we would like to thank all the people and organizations that have participated in and supported MCAI 2023. Sincere thanks to all the authors and editorial board members who have contributed to this Proceedings. Through the publication and dissemination of the Proceedings, we can facilitate the cooperation between academia and industry, promote the translation and application of scientific research results, and contribute to the solution of practical problems.The Committee of MCAI 2023List of Committee Member is available in this pdf.

Karyotypic stasis and its implications for extensive hybridization events in corallivores species of butterflyfishes (Chaetodontidae)

The butterflyfishes (Chaetodontidae), emblematic inhabitants of coral reef environments, encompass the majority of known coralivorous species and show one of the highest hybridization rates known among vertebrates, making them an important evolutionary model. The vast knowledge about their life history and phylogenetic relationships contrasts with scarce information on their karyotype evolution. Aiming to expand the cytogenetic data of butterflyfishes and evaluate their karyotype evolution in association with evolutionary aspects, we conducted an extensive cytogenetic analysis in 20 species (Heniochus pleurotaenia and 19 Chaetodon spp.) from the Atlantic and Indo-Pacific regions, comparing the karyotype macrostructure and the arrangement of the 18S and 5S rDNA repetitive DNA classes in their chromosomes. The results demonstrate that butterflyfishes underwent a period of karyotypic stasis, as evidenced by their homoploid and structurally identical basal karyotype, which has 2n = 48 acrocentric chromosomes and is shared by 90% of species. Only C. trifascialis (2n = 48; FN = 50) and C. andamanensis (2n = 48; FN = 52) stood out because they both had karyotypes that diverged due to pericentric inversions. The microstructural arrays of 18S rDNA and 5S rDNA sequences were primarily comprised by single and independent loci on homologous chromosomes, indicating that there was little reshuffling among sets of orthologue chromosomes of species. Geographical comparisons revealed similar karyotypes between individuals of C. striatus from the Greater Caribbean and those of the coast of Brazil, corroborating previous data of gene flow through Amazon/Orinoco plume. The conservative chromosomal patterns in the butterflyfishes, likely overcome the limitations related to segregation and pairing of heterospecific complements and reinforce their contribution to the high degree of hybrid viability and introgression in Chaetodon species.

Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae

Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features related to Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.

A new winter wheat genetic resource harbors untapped diversity from synthetic hexaploid wheat

Key messageThe NIAB_WW_SHW_NAM population, a large nested association mapping panel, is a useful resource for mapping QTL from synthetic hexaploid wheat that can improve modern elite wheat cultivars.The allelic richness harbored in progenitors of hexaploid bread wheat (Triticum aestivum L.) is a useful resource for addressing the genetic diversity bottleneck in modern cultivars. Synthetic hexaploid wheat (SHW) is created through resynthesis of the hybridisation events between the tetraploid (Triticum turgidum subsp. durum Desf.) and diploid (Aegilops tauschii Coss.) bread wheat progenitors. We developed a large and diverse winter wheat nested association mapping (NAM) population (termed the NIAB_WW_SHW_NAM) consisting of 3241 genotypes derived from 54 nested back-cross 1 (BC1) populations, each formed via back-crossing a different primary SHW into the UK winter wheat cultivar ‘Robigus’. The primary SHW lines were created using 15 T. durum donors and 47 Ae. tauschii accessions that spanned the lineages and geographical range of the species. Primary SHW parents were typically earlier flowering, taller and showed better resistance to yellow rust infection (Yr) than ‘Robigus’. The NIAB_WW_SHW_NAM population was genotyped using a single nucleotide polymorphism (SNP) array and 27 quantitative trait loci (QTLs) were detected for flowering time, plant height and Yr resistance. Across multiple field trials, a QTL for Yr resistance was found on chromosome 4D that corresponded to the Yr28 resistance gene previously reported in other SHW lines. These results demonstrate the value of the NIAB_WW_SHW_NAM population for genetic mapping and provide the first evidence of Yr28 working in current UK environments and genetic backgrounds. These examples, coupled with the evidence of commercial wheat breeders selecting promising genotypes, highlight the potential value of the NIAB_WW_SHW_NAM to variety improvement.

Sub-Nanomolar Detection of Oligonucleotides Using Molecular Beacons Immobilized on Lightguiding Nanowires.

The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by immobilizing them on lightguiding nanowires. Upon hybridization to a complementary oligonucleotide, the fluorescence from the surface-bound beacon becomes coupled in the lightguiding nanowire core and is re-emitted at the nanowire tip in a narrower cone of light compared with the standard 4π emission. Prior knowledge of the nanowire positions allows for the continuous monitoring of fluorescence signals from each nanowire, which effectively facilitates the discrimination of signals arising from hybridization events against background signals. This resulted in improved signal-to-background and signal-to-noise ratios, which allowed for the direct detection of oligonucleotides at a concentration as low as 0.1 nM.

Spontaneous hybridization among invasive Poaceae in Hawai‘i: Chloris × pseudosagrana nothosp. nov. and Cenchrus × peregrinus nothosp. nov.

During grass surveys across the islands of Hawai‘i in 2022, two novel hybrids among non-native Poaceae were found growing on roadsides. Spontaneous hybridization was observed among Chloris barbata and C. divaricata on O‘ahu and among Cenchrus clandestinus and C. setaceus on Hawai‘i island. Morphological evidence initially suggested these plants may be hybrids and molecular analysis using the ITS and rpl32-trnL regions confirmed that the plants are hybrids and identified their parentage. These hybrids are named Chloris × pseudosagrana nothosp. nov. and Cenchrus × peregrinus nothosp. nov. No developed seeds could be found on either of these hybrids and they are suspected to be sterile F1 hybrids. The occurrence of hybridization events among other non-native species are also discussed.

Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia.

Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.

Evolutionary relationships, hybridization and diversification under domestication of the locoto chile (Capsicum pubescens) and its wild relatives.

Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C.eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C.cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.

Characterization of the cryptic interspecific hybrid Lemna × mediterranea by an integrated approach provides new insights into duckweed diversity.

Lemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms. Although molecular taxonomy has helped clarify the phylogenetic history of this family, some inconsistency with morphological data leads to frequent misclassifications in the genus Lemna. Recently, the finding that Lemna japonica is an interspecific hybrid between Lemna minor and Lemna turionifera, provided a clear explanation to one of such taxonomic questions. Here we demonstrated that L. minor is also capable to hybridize with Lemna gibba, generating a cryptic but widespread taxon in the Mediterranean area. The nothotaxon Lemna × mediterranea is described and compared with clones of the putative parental species L. minor and L. gibba. Genetic analysis by nuclear and plastid markers, as well as genome size measurement, revealed that two different cytotypes, diploid and triploid, originated by at least two independent hybridization events. Despite high overall similarity, morphometrical, physiological and biochemical analyses showed an intermediate position of L. × mediterranea between its parental species in most qualitative and quantitative characters, and also separation of the two hybrid cytotypes by some criteria. These data provide evidence that hybridization and polyploidization, driving forces of terrestrial plant evolution, contribute to the duckweed genetic diversity and may have shaped the phylogenetic history of these mainly asexual, aquatic plants.

Thepparatia vines (Hibisceae subtribe Trionum) phylogenomics and evolution

Abstract Hibisceae subtribe Trionum is the largest clade within Hibiscus s.l. and contains genera with a wide range of growth forms: herbaceous (Abelmoschus), shrubs (Malvaviscus), trees (Wercklea), and exceptionally lianas. The rare and localized Thepparatia species are unique in that they combine a lianescent habit and trioecy. Several problems have delayed the study of Hibisceae classification including low genetic variability, lack of synapomorphic morphological characters, transoceanic dispersal events, and allopolyploidy. Here, we present a comprehensive phylogenomic hypothesis of Thepparatia based on analyses of the maternally inherited chloroplast and biparentally inherited nuclear ribosomal cistron sequences, and compare these results with its speciation, karyology, and breeding system. Chloroplast genomes in subtribe Trionum were highly conserved except in Abelmoschus where four additional genes were duplicated. Recent diploid interspecific hybridization is suggested in Thepparatia sipsongpannaensis between T. fragrans and T. scandens during the Pleistocene, around 640 000 years ago. Our observations also indicate Thepparatia have a trioecious breeding system that combined with a unique habit, and a highly localized distribution pattern, have created cross-pollination barriers and ecological specialization. This suggests hybridization events are rare but evolutionary significant in subtribe Trionum. Finally, our study supports important nomenclature changes: the synonymization of Hibiscus austroyunnanensis with Thepparatia fragrans and the publication of a new species, Thepparatia sipsongpannaensis.

Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree (Davidia involucrata) revealed by whole genome resequencing

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.