Panax (Araliaceae) is a small genus with several well known medicinally important species. It has a disjunct distribution between eastern Asia and eastern North America, with most species from eastern Asia, especially the Himalayan – Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was likely widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of southwest China and tropical Indochina, where some taxa migrated northwestward to the Himalayan-Hengduan Mountains, eastward to central and eastern China, and then onward towards Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng+P. japonicus+P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

Understanding plant diversity and the phylogenetic divergences in the Northern Hemisphere is essential for in-depth evolutionary studies and conservation efforts. Maianthemum is an ideal example to explore plant diversification processes in the Northern Hemisphere, with more than 35 species widely distributed in forests in North to Central America, Europe and eastern Asia. Yet the phylogenetic relationships within Maianthemum remain elusive. In this study, we reconstructed a well-supported phylogenetic framework of Maianthemum and explored possible gene introgressions and reticulate evolution using nuclear and chloroplast genomes based on the target enrichment Hyb-Seq approach. Both nuclear and chloroplast phylogenetic results supported three clusters corresponding to their biogeographic distribution of the New World, the Himalayan - Hengduan Mountains (HHM), and the north temperate zone, respectively. The genus was inferred to be most likely originated in the North America with migrations into central America and eastern Asia in the late Miocene. Our results suggested that both incomplete lineage sorting and hybridizations/introgressions along with geographic isolation have contributed to the rapid divergence of Maianthemum in eastern Asia, which may represent a complex model for the evolutionary radiation of plants in eastern Asia and even the Northern Hemisphere.

Rich materials can provide more opportunities for exploring the mechanisms of speciation driven by sexual selection. Being the fastest-evolving arthropods to date, Nudilla Gorochov, 1988 (= Laupala Otte, 1994) are primarily responsible for their rapid divergence due to the variability of their calling songs (sexual signals). In addition, they also exhibit morphological conservatism, with little variation between species. Similar circumstances can be seen in tree crickets, which have conservative morphology and a diverse range of song variations. Thus, we believe that tree crickets could serve as a model for research on sexual selection since they share a similar evolutionary history and mode of differentiation with Nudilla. However, due to the improper methods in analyzing the calling songs and nearly identical morphological features between taxa, there are many problems with the taxonomy of Oecanthinae in China. To solve these problems, we conducted an integrative taxonomic study of Chinese Oecanthinae based on comparative morphology, species delimitation, acoustical analysis, and phylogenetic analysis. The study confirmed twelve species of Oecanthinae in China, including four new species, and recognized one new synonym and two misidentifications. Meanwhile, we confirmed the morphological stability of Oecanthinae, and revealed that variation in color, size, and morphology may be intraspecific polymorphism, which sometimes does not reflect the species relationships. The result indicates that the acoustic parameter freq.median can be used for efficient and accurate species delimitation in Oecanthinae. We speculate that incomplete species divergence leads to complexity in species relationships at the genetic level of Oecanthinae. The conservation of morphological characters, the interspecificity of songs and the complexity of species relationships suggest that sexual selection have played a role in the evolution of Oecanthinae. Our study resolves some systematic and taxonomic problems of Oecanthinae, clarifies the species relationships of Oecanthinae in China, and provides clues for expanding the cricket groups to be used in speciation studies.

Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitat-adapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing, however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (6 species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section-based backbone phylogenies of Oxalis. However, a closer look at the phylogeny of sect. Carnosae revealed non-monophyletic arrangements involving O. megalorrhiza and O. bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear SSR markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic and biogeographic studies in Oxalis.

Gene duplications have contributed to the innovation of morphological traits during plant evolution. An outstanding example is the role of CYCLOIDEA2 (CYC2) gene duplications in the formation of the complex structure of Asteraceae capitula. Previous studies have shown that Chrysanthemum lavandulifolium and a few other species of the Asteraceae harbor two copies of CYC2e. Here, we identified a lineage-specific CYC2e duplication event at the root of the phylogeny of the tribe Anthemideae by analyzing the evolutionary history of CYC2 genes across the Asteraceae. Although the gene expression patterns of CYC2e1 and CYC2e2 were similar in most of floral organs, CYC2e1 promoted ligule elongation by promoting cell expansion, whereas CYC2e2 exhibited a weak inhibiting effect on the ray-floret development, and overexpression of CYC2e2 resulted in the maldevelopment of stamens in disc florets. These results indicated differentiated functions of CYC2e1 and CYC2e2 in the capitulum development of the Anthemideae. Given the previous data that demonstrated CYC2g and CYC2d as main regulators in ligule morphogenesis, we comparatively analyzed 10 Asteraceae genomic data, and identified tandem arrays of CYC2g, CYC2d and CYC2e. We further investigated the regulatory relationships between CYC2g/CYC2d and CYC2e genes, and found that CYC2g can activate the expression of CYC2e1. The findings of this study elucidate the synergistic roles of CYC2 genes in regulating the formation of the Asteraceae capitula and enhance understanding of the mechanism of duplicated gene retention during plant evolution.

Koelerioid grasses (subtribe Aveninae, tribe Poeae; Pooideae) resolve into two major clades, here called Koelerioid Clade A and Clade B. Phylogenetic relationships among koelerioid grasses are investigated using plastid DNA sequences of rpl32‐trnL, rps16‐trnK, rps16 intron, and ITS regions, focusing on Trisetum, Acrospelion, and some annual species (Rostraria p.p. and Trisetaria p.p.) closely related to Trisetum flavescens in Koelerioid Clade A. Phylogenetic analyses of several selected data sets performed for 80 taxa and using Maximum Likelihood and Bayesian methods, revealed mostly congruent topologies in the nuclear and plastid trees, but also reticulation affecting several lineages. Trisetum is restricted to one species, Trisetum flavescens, which is sister to the clade formed by Trisetum gracile and Trisetaria aurea. The latter two species are classified here in the genus Graciliotrisetum gen. nov. The sister clade includes three species of Rostraria and Trisetaria lapalmae, all of which are classified here in a resurrected genus, Aegialina, which includes four species. Acrospelion is enlarged to include 13 species after the addition of other species formerly classified in Trisetum sect. Trisetum and T. sect. Acrospelion. We also transfer Trisetum ambiguum, T. longiglume, and Koeleria mendocinensis to Graphephorum; and Helictotrichon delavayi to Tzveleviochloa, expanding these genera to eight and six species, respectively. We evaluate cases of reticulate evolution between Koelerioid Clades A and B and within Koelerioid Clade A, which probably gave rise to Graphephorum, Rostraria cristata and Rostraria obtusiflora, respectively. Finally, we comment on polyploidy and biogeographic patterns in koelerioid grasses. We propose the following 26 new combinations: Acrospelion alpestre, A. altaicum, A. argenteum, A. bertolonii, A., buschianum, A. buschianum ssp. transcaucasicum, A. fuscum, A. laconicum, A. macrotrichum, A. rigidum, A. rigidum ssp. teberdense, A. tamonanteae, A. velutinum, Aegialina lapalmae, A. pubescens, A. pumila, A. pumila ssp. fuscescens, A. salzmannii, A. salzmannii ssp. cossoniana, Graciliotrisetum aureum, G. gracile, Graphephorum ambiguum, G. longiglume, G. mendocinense, G. orthochaetum, and Tzveleviochloa delavayi. Lectotypes are designated for the names Aegialitis tenuis, Aira melicoides, Avena aspera var. parviflora, Avena delavayi, Koeleria grisebachii var. mendocinensis, K. pubescens ssp. cossoniana, K. pumila, K. salzmannii, Phalaris pubescens, Trisetum aureum, T. cernuum, T. fuscescens, T. longiglume and, T. wolfii; and we designate one neotype for Alopecurus litoreus.

Fossil wood is one of the crucial proxies for understanding terrestrial vegetation composition and development in Earth history. The gymnosperm wood taxon Xenoxylon Gothan is a significant member of the Mesozoic flora. To date, more than 20 species of Xenoxylon have been described, exclusively from Laurasia. However, its botanical affinities have remained enigmatic ever since it was described, over a century ago. Here we perform a phylogenetic analysis of Xenoxylon to understand the systematic relationship with extant conifers. Data come from four nucleotide regions (trnL-F, trnK-matK, rbcL, psbA-trnH), xylological characters, and biomolecular composition of five extant conifer families; for Xenoxylon, no nucleotide data are available. Using maximum parsimony in TNT (Tree Analysis using New Technology), Xenoxylon appeared basal to Araucariaceae in the dataset combining genes and xylological characters, whereas Xenoxylon is placed next to Podocarpaceae in the dataset combining genes and biomolecular characters. To find a reliable systematic placement of Xenoxylon, a combined dataset of genes, xylological and biomolecular characters is analyzed. Our results and interpretations indicate that Xenoxylon is closely related to Podocarpaceae. This first phylogenetic analysis of Xenoxylon fills the knowledge gap of the systematic relationship of this taxon and contributes to a better understanding of the evolution of extant Podocarpaceae.

The orchid Dactylorhiza cantabrica H.A. Pedersen is a narrow endemic occurring at western Cantabrian Mountains in NW Spain. Previous allozyme and morphological studies suggest that it might result from the hybridization of two widespread congeners: the triploid D. insularis and the diploid D. sambucina. However, this hypothesis has not been tested using multiple genetic markers, necessary to analyse phylogenies in complex genera such as Dactylorhiza. In this study, the Hyb-Seq technique is applied together with the universal Angiosperms353 probe kit to sequence multiple plastid and low-copy nuclear genes. The phylogenetic relationships between the three species, estimated based on 269 and 266 nuclear genes under concatenation and coalescent-based approaches, respectively, revealed highly-supported clades containing each putative parent, D. insularis and D. sambucina. The position of D. cantabrica was not well resolved, suggesting the existence of mixed inheritance, where different genes come from each parent. Phylogenetic networks, used for visualizing the conflict between nuclear gene trees, placed D. cantabrica between the two parents and revealed high levels of reticulation. In addition, nuclear genetic variation within and among species was explored with allele frequencies-based tools further supporting the intermediate position of D. cantabrica and the hypothesis of a recent hybrid origin. Finally, 75 plastid genes revealed that D. insularis might be the maternal donor. Altogether, our results point to the allopolyploid origin of D. cantabrica from D. insularis and D. sambucina, as well as to the clear genetic differentiation of the two parental species.

Aquilaria (Thymelaeaceae), a tropical and subtropical plant, is one of the main genera that can produce agarwood. Aquilaria sinensis and A. yunnanensis are native Chinese tree species, and A. sinensis is China's main agarwood source. Agarwood is a non-timber forest product with high economic and medicinal value. First-grade agarwood is sold as much as $100,000 per kilogram. There has been little research on the saprobic fungi associated with Aquilaria, with only eleven records having been reported. In the present study, ten terrestrial saprobic fungi associated with A. sinensis and A. yunnanensis were collected in China. Based on morphological and phylogenetic studies, these ten collections are introduced herein as one new genus (Aquilariomyces), nine new species—Aquilariomyces aquilariae, Corynespora aquilariae, Melomastia maomingensis, Nigrograna aquilariae, Parathyridariella aquilariae, Peroneutypa maomingensis, Phaeoseptum aquilariae, Pseudothyridariella aquilariae, and Triangularia aquilariae, and one known species (Camarographium clematisidis). Descriptions, illustrations of morphological characteristics, photo plates, phylogenetic trees, and the results of a pairwise homoplasy index test (PHI) test results are provided.

Rhododendron is a significant plant genus, with over 600 identified species in China. The subgenus Hymenanthes holds the largest number of Rhododendron germplasms and showcases strong environmental adaptability. However, there remains a lack of understanding regarding Rhododendron’s evolution and environmental adaptations. R. bailiense, an exceedingly rare species, thrives in the alkaline karst landforms of Guizhou, southwest China, different to the typical growing environment of other Rhododendrons. In this study, we present a chromosome-level genome assembly of R. bailiense, revealing a genome size of 923.3 Mb, a contig N50 of 24.5 Mb, and a total of 47,567 predicted genes. An evolutionary analysis indicated that R. bailiense diverged from its ancestors prior to other subgenus Hymenanthes Rhododendrons, with the expanded and contracted genes being notably enriched in 'stress response' and 'growth', respectively. R. bailiense is predominantly found on limestone soil in the mountains of Guizhou, with only two wild populations known. The genome of R. bailiense contained a high copy number of ankyrin repeats (ANKs) and Ca²⁺-ATPases (CAPs) genes, primarily involved in Ca²⁺ transport, shedding light on how R. bailiense copes with karst high-calcium stress. In contrast, the structures of the ANKs displayed unique characteristics, while the CAPs exhibited conservatism. The R. bailiense genome provides new insights into the adaptation and evolutionary history of Rhododendron plants in karst environments, proving valuable for adaptive breeding and ecological enhancement in such challenging settings.

During the Cretaceous period, the lacewing superfamily Mantispoidea, with an assemblage of species possessing raptorial forelegs, have undergone a rapid species radiation, characterized by abundant species richness and high morphological plasticity. Nevertheless, the morphology and early evolution of the specialized predatory organ around the time of its origin in raptorial Mantispoidea have been poorly documented due to the rarity of fossil evidence, especially for the pre-Cretaceous fossils. Herein, a new genus and new species, i.e. Archarhachiberotha longitarsa J. Wang, Ren et Y. Wang gen. et sp. nov., was described from the Middle Jurassic Jiulongshan Formation of northeastern China. This new genus was characterized by the remarkable raptorial forelegs, i.e. typically elongated coxa, relatively less-swollen femur and rudimentary small femoral spines, and well-developed tarsi. Considering the peculiar morphological combination and antiquity of the new genus, it was assigned to be a stem-group lineage of Mantispoidea. Besides, the detailed analyses of morphology and biological functions of raptorial forelegs were made to conclude that the new genus evolved into an unknown but primitive raptorial type that was distinctly different from the extant morphological features and raptorial mechanisms. In addition, the evolutionary tendency of raptorial Mantispoidea herein summarized highlights morphological diversity and disparity between fossil and extant representatives, and provides a rare case to explore the entire evolutionary history of a specialized structure in one lineage. 

The genus Didymocarpus Wall is a core group of the subfamily Didymocarpoideae in Gesneriaceae with a complex taxonomic history. It has long been controversial to delimit Didymocarpus and its allies. We conducted phylogenetic reconstructions with high-density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (ETS, ITS, 18S, 26S) and five chloroplast DNAs (atpB-rbcL, rpl16, rps16, trnH-psbA, trnL-F). The results demonstrate that both Didymocarpus and Allocheilos are not monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitate the range of the Didymocarpus s. str. with two-section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution that are found only in the southeastern China. In addition, we also proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera.

Eucalypt fossils were widely reported from the Cenozoic deposits across the Southern Hemisphere (Australia, New Zealand, and Argentina). However, no attached reproductive and vegetative fossil remains of this myrtaceous clade have been discovered till now. We report and describe for the first time a fossil eucalypt twig with attached foliage, flower buds, and mature flowers from the early Eocene (~55–52 Ma) sediments (Palana Formation) of Rajasthan, western India. As both vegetative and reproductive organs are in organic connection, they clearly represent the same species. In addition, here we also introduce fossil materials of isolated leaves, flower buds, inflorescence, and flowers recovered from the same stratigraphic level. Morphological similarities that relate our Eocene fossils to extant members of the eucalypt clade include robust, thick petiolate lanceolate-shaped leaves with intramarginal secondary veins; operculate flower buds consisting of imbricate petals with discernable margins; solitary inflorescence with 3 flowers per umbellaster, epigynous and bisexual flowers. Based upon combined characteristics of leaf, flower, and bud morphology, these fossils conform to the Eucalypt clade and are recognized as a new fossil genus and species Hindeucalyptus eocenicus Patel, R.F. Almeida, Ali et Khan, gen. nov. et sp. nov. We also compare it with extant and extinct eucalypts using morphological phylogeny and character mapping analyses. In addition, we briefly discuss its phytogeographic and paleoclimatic implications regarding the distribution and habitat of fossil and modern eucalypts.

The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome-based macro-evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a dataset of more than 569,990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole-genomes and transcriptomes so far, we compared the performance of different data matrices with universal-single-copy orthologs (USCO). The resultant trees based on different datasets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750-abs80) provided well-resolved topology. The analyses confirm that Cucujoidea sensu Robertson et al. 2015 is a non-monophyletic group, consisting of Erotyloidea, Nitiduloidea and Cucujoidea sensu Cai et al. 2022. Moreover, Erotyloidea is the early-diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well-resolved higher-level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.

Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, D. floribunda, D. yunnanensis and D. elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population-level genomic data (RAD-SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensis-D. floribunda group, but with cyto-nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil-calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD-SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai-Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid- Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome-scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.

The two invasive Reynoutria species, R. japonica var. japonica, R. sachalinensis and their hybrid R. x bohemica are often misidentified by managers and non-specialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations, in terms of morphology, genetic diversity and ploidy level. We resolved the identity of North-Eastern French invasive populations using 4,582 SNPs from a RADseq analysis, DNA contents estimated by flow cytometry and 12 vegetative morphometric variables. The SNPs supported only one single genotype for R. japonica over 11 localities, while the nine localities of R. x bohemica represented by one genotype each. Estimation of genome size using DAPI-staining and flow cytometry revealed only octoploid cytotypes for R. japonica and hexaploid cytotypes for R. x bohemica, whereas R. sachalinensis was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base and apex shape, and the extrafloral nectaries on the node.

Astragalus (Fabaceae) is astoundingly diverse in temperate, cold arid regions of Earth, positioning this group as a model clade for investigating the distribution of plant diversity in the face of environmental challenge. Here we identify the spatial distribution of diversity and endemism in Astragalus, using species distribution models for 752 species and a phylogenetic tree comprising 847 species. We integrated these to map centers of species richness (SR) and relative phylogenetic diversity (RPD) and used randomization approaches to investigate centers of endemism. We also used clustering methods to identify phylogenetic regionalizations. We then assembled predictor variables of current climate conditions to test environmental factors predicting these phylogenetic diversity results, especially temperature and precipitation seasonality. We find that SR centers are distributed globally at temperate middle latitudes in arid regions, but the Mediterranean Basin is the most important center of RPD. Endemism centers also occur globally, but Iran represents a key endemic area with a concentration of both paleo- and neoendemism. Phylogenetic regionalization recovered an east-west gradient in Eurasia and an amphitropical disjunction across North and South America; American phyloregions are overall most closely related to east and central Asia. SR, RPD, and lineage turnover are driven mostly by precipitation and seasonality, but endemism is driven primarily by diurnal temperature variation. Endemism and regionalization results point to western Asia and especially Iran as a biogeographic gateway between Europe and Asia. RPD and endemism highlight the importance of temperature and drought stress in determining plant diversity and endemism centers.

Taxonomy of Populus is a challenging task, especially in regions with complex topography, such as the Qinghai-Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the Flora of China, P. pseudoglanca and P. wuana are classified into sect. Leucoides and sect. Tacamahaca, respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of Populus on the plateau, we found 31 taxa from the two sections. Through identification based on morphology and habitats, we confirmed that the “P. pseudoglanca” recorded in the Flora of Sichuan is not true P. pseudoglanca, while P. pseudoglanca and P. wuana recorded in the Flora of China may refer to the same species. By performing whole-genome re-sequencing of 150 individuals from the 31 taxa, we derived 2.28 million SNPs. Further genetic and phylogenetic analyses demonstrated that the genetic structure of P. wuana is extremely consistent with P. pseudoglanca, and they all originate through the natural hybridization between P. ciliata in sect. Leucoides and P. curviserrata in sect. Tacamahaca. Our results suggested that P. wuana should be merged with P. pseudoglanca taxonomically. This study not only clarifies the taxonomic confusions related to P. pseudoglanca and P. wuana but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.

The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time-calibrated phylogeny for 749 species representing c. 80% of the genera of this clade using nrDNA ITS, plastid matK, and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade’s temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil-calibrated dating analysis showed a nearly simultaneous divergence of the stem node [c. 62 million years ago (Ma)] and the crown node (c. 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c. 10 Ma. Possible explanations for the present-day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra- and intercontinental long-distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid-Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.

Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti-aging, anti-inflammatory and anti-oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near-complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of LTR contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole-genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with diseases tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in root, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.

Jujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 non-redundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast-to-nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species.

The most significant driver of adaptive radiation in the New World leaf-nosed bats (Phyllostomidae) is their remarkably diverse feeding habits, yet there remains a notable scarcity of studies addressing the genetic underpinnings of dietary diversification in this family. In this study, we have assembled a new genome for a representative species of phyllostomid bat, the fringe-lipped bat (Trachops cirrhosis), and integrated it with eight published phyllostomid genomes, along with an additional 10 genomes of other bat species. Comparative genomic analysis across 10,200 orthologus genes has unveiled that those genes subject to divergent selection within the Phyllostomidae clade are notably enriched in metabolism-related pathways. Furthermore, we identified molecular signatures of divergent selection in the bitter receptor gene Tas2r1, as well as 14 genes involved in digesting key nutrients such as carbohydrates, proteins, and fats. In addition, our cell-based functional assays conducted on Tas2r1 showed a broader spectrum of perception for bitter compounds in phyllostomids compared to non-phyllostomid bats, suggesting functional diversification of bitter taste in Phyllostomidae. Together, our genomic and functional analyses lead us to propose that divergent selection of genes associated with taste, digestion and absorption, and metabolism assumes a pivotal role in steering the extreme dietary diversification in Phyllostomidae. This study not only illuminates the genetic mechanisms underlying dietary adaptations in Phyllostomidae bats but also enhances our understanding of their extraordinary adaptive radiation.

The genus Xylaria comprises a diverse group of fungi with a global distribution and significant ecological importance, known for being a source of bioactive secondary metabolites with antibacterial, antioxidative, anti-carcinogenic, and additional properties. In this study, we present a comprehensive taxonomic revision of the species of Xylaria found in some parts of southern China, characterized by an extensive multilocus phylogeny analysis based on internal transcribed spacer (ITS), TUB2 (β-tubulin), and RNA polymerase II second largest subunit (rpb2) gene regions. Morphological examination and detailed comparative analyses of the collected specimens were conducted to determine the distinctiveness of each species. The multilocus phylogeny approach allowed us to infer evolutionary relationships and assess species boundaries accurately, leading to the identification of 40 novel Xylaria species hitherto unknown to science. The newly described species are: X. baoshanensis, X. bawanglingensis, X. botryoidalis, X. dadugangensis, X. doupengshanensis, X. fanglanii, X. glaucae, X. guizhouensis, X. japonica, X. jinghongensis, X. jinshanensis, X. kuankuoshuiensis, X. liboensis, X. negundinis, X. orbiculati, X. ovata, X. pseudoanisopleura, X. pseudocubensis, X. pseudobambusicola, X. pseudoglobosa, X. pseudohemisphaerica, X. pseudohypoxylon, X. puerensis, X. qianensis, X. qiongzhouensis, X. rhombostroma, X. serratifoliae, X. shishangensis, X. shuqunii, X. shuangjiangensis, X. sinensis, X. tongrenensis, X. umbellata, X. xishuiensis, X. yaorenshanensis, X. yinggelingensis, X. yumingii, X. yunnanensis, X. zangmui, and X. zonghuangii. The study's findings shed light on the distinctiveness of the newly described species, supported by both morphological distinctions and phylogenetic relationships with their close relatives. This taxonomic revision significantly contributes to our understanding the diversity of Xylaria in China and enriches the knowledge of fungal biodiversity worldwide.

Understanding the richness and diversification processes in the Mediterranean basin requires both knowledge of the current environmental complexity, paleogeographic and paleoclimate events and information from studies that introduce the temporal dimension. The Carthamus-Carduncellus complex (Cardueae, Compositae) constitutes a good case study to investigate the biogeographic history of this region because it evolved throughout the basin. We performed molecular dating, ancestral area estimation and diversification analyses based on previous phylogenetic studies of a nearly complete taxon sampling of the complex. The main aims were to determine the role of tectonic and climatic events in the disjunction of the complex and the expansion route of the two main lineages, Carduncellus s.l. and Carthamus. Our results suggest that the main lineages in the complex originated during the Miocene. Later, all main paleogeographic and paleoclimatic events during the Neogene and Pleistocene in the Mediterranean basin had an important imprint on the evolutionary history of the complex. The Messinian Salinity Crisis facilitated the dispersion of the genus Carduncellus from North Africa to the Iberian Peninsula and the split of the genera Phonus and Femeniasia from the Carduncellus lineage. The onset of the Mediterranean climate in the Pliocene together with some orogenic processes could be the main causes of the diversification of the genus Carduncellus. In contrast, Pleistocene glaciations played a key role in the species diversification of Carthamus. In addition, we emphasize the problems derived from secondary dating and the existing differences between two previous dating analyses of the tribe Cardueae.

Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node-dating (ND) based on plastomes of all eight extant species and tip-dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% HPD: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant events without fossils, but as many as to six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via Bering Land Bridge during the early Oligocene and the early Miocene. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except P. fraxinifolia and P. stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change.

The Sui people living in Guizhou province have a unique ethnic culture and population history due to their long-time isolation from other populations. To investigate the genetic structure of Sui populations in different regions of Guizhou, we genotyped 89 individuals from 4 Sui populations using genome-wide SNP arrays. We analyzed the data using principal component analysis (PCA), ADMIXTURE analysis, f-statistics, qpWave/qpAdm, TreeMix analysis, fineSTRUCTURE, and GLOBETROTTER. We found that Sui populations in Guizhou were genetically homogeneous and had a close genetic affinity with Tai-Kadai-speaking populations, Hmong-Mien-speaking Hmong, and some ancient populations from southern China. The Sui populations could be modeled as an admixture of 33.5%-37.9% of Yellow River Basin farmer-related ancestry and 62.1%-66.5% of Southeast Asian-related ancestry, indicating that the southward expansion of northern East Asian-related ancestry influenced the formation of the Tai-Kadai-speaking Sui people. Future publications of more ancient genomics in southern China could effectively provide further insight into the demographic history and population structure of the Sui people.

The geodiversity of rocky ecosystems includes diverse plant communities with specific names, but their continental-scale floristic identity and the knowledge on the role of macroclimate remain patchy. Here we assessed the identity of plant communities in eastern Brazil across multiple types of rocky landscapes and evaluated the relative importance of climatic variables in constraining floristic differentiation. We provided lists of diagnostic species and an assessment of the conservation status of the identified floristic groups. We compiled a dataset of 151 sites (4,498 species) from rocky ecosystems, including campos rupestres, campos de altitude, granitic-gneiss lowland inselbergs and limestone outcrops. We used unsupervised clustering analysis followed by ANOSIM to assess floristic groups among sites. We performed a random forest variable selection to test whether the identified floristic groups occupy distinct climatic spaces. Six groups (lithobiomes) segregated floristically according to lithology and climate. Alongside campos de altitude and limestone outcrops, inselbergs were divided according to the biome in which they occur (Atlantic Forest or Caatinga) and campos rupestres were largely segregated according to their lithological matrix (ironstone or quartzitic). Plant communities of Caatinga inselbergs were more similar to limestone outcrops, while Atlantic Forest inselbergs communities resembled campos de altitude. The composition of plant communities on outcrops seems to be largely constrained by lithology, but climatic factors are also meaningful for sites with similar lithology. The current network of protected areas does not cover these unique ecosystems and their floristic heterogeneity, with protection least adequate for Caatinga inselbergs, ironstone campos rupestres and limestone outcrops.

The general dynamic model of oceanic island biogeography (GDM) views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, Cyrtandra, and inferred directionality of dispersal and founder events throughout the four biogeographical units of the Indo-Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of Cyrtandra in the Southeast Asian grade showed early bursts followed by a plateau which is consistent with adaptive radiation. We did not detect signals of diversity-dependent diversification and this is attributed to Southeast Asian cyrtandras occupying various niche spaces, evident by its wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model, wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step towards a framework for investigating diversification dynamics as predicted by GDM in highly successful insular taxa.

Crop wild relatives (CWRs) of cultivated species may provide a source of genetic variation that can contribute to improving product quantity and quality. To adequately use these potential resources, it is useful to understand how CWRs are related to the cultivated species and to each other to determine how key crop traits have evolved and discover potentially usable genetic information. The chocolate industry is expanding and yet is under threat from a variety of causes including pathogens and climate change. Theobroma cacao L. (Malvaceae), the source of chocolate, is a representative of the tribe Theobromeae that consists of four genera and c. 40 species that began to diversify over 25 million years ago. The great diversity within the tribe suggests that its representatives could exhibit advantageous agronomic traits. In this study, we present the most taxonomically comprehensive phylogeny of Theobromeae to date. DNA sequence data from WRKY genes were assembled into a matrix that included 56 morphological characters and analyzed using a Bayesian approach. The inclusion of a morphological dataset increased resolution and support for some branches of the phylogenetic tree. The evolutionary trajectory of selected morphological characters was reconstructed onto the phylogeny. This phylogeny provides a framework for the study of morphological and physiological trait evolution which can facilitate the search for agronomically relevant traits.

The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1438 to 1870 species within approximately 130 genera predominantly distributed from northern Canada to Patagonia. Four centers of diversity from Central and North America (Chihuahua, Puebla-Oaxaca, Sonora-Sinaloan and Jalisco) and three centers of diversity from South America (Southern central Andes, Caatinga and Mara Atlantica) have played a pivotal role in disbursing cacti around the globe. Mexico is considered the richest area in cacti species with close to 563 species grouped into 50 genera. Approximately 118 species have been domesticated by Mesoamerican people as food crops and for ornamental purposes. Cacti inhabit a wide range of ecosystems and climate regions, ranging from tropical to subtropical and from arid to semiarid regions. Species belonging to the genus Opuntia are the major food crop producers in the family. Cacti have derived characteristics from familial synapomorphies within the Caryophyllales. Reproduction occurs through pollination facilitated by birds, bats, bees and other insects. Climate variability, whether natural or human induced, threaten global crop production including high temperatures, salinity, drought, flood, changes in soil pH and urbanization. Cacti have several adaptations that are important for coping with abiotic stresses, such as crassulacean acid metabolism (CAM photosynthesis), as well as modifications to root and stem physiological pathways. This review aims to provide a comprehensive view of the fruit crops in Cactaceae, including the evolution, worldwide distribution, and the environmental factors impacting cultivation.

Islands in the tropical Pacific Ocean are renowned for high biodiversity and endemism despite having relatively small landmasses. However, our knowledge of how this biodiversity formed remains limited. The taxon cycle, where well-dispersed, earlier colonizers become displaced from coastal to inland habitats by new waves of colonizers, producing isolated, range-restricted species, has been proposed to explain current biodiversity patterns. Here, we integrate the outcomes of phylogenetic studies in the region to investigate the sources, age, number of colonizations, and diversification for 16 archipelagos in the tropical and subtropical South Pacific. We then evaluate whether results support the taxon cycle as a plausible mechanism for these observations. We find that most species in the Pacific arrived within the last 5 million years from geographically close sources, suggesting that colonization by new taxa is a frequent and ongoing process. Therefore, our findings are broadly consistent with the theory of the Taxon Cycle, which posits that ongoing colonization results in the gradual displacement of established lineages. Only the oldest archipelagos, New Caledonia and Fiji, do not conform to this trend, having proportionally less recent colonization events, suggesting that the taxon cycle may slow on older islands. This conclusion is further validated by New Caledonia having lower diversification rate estimates than younger islands. We found that diversification rates across archipelagos are negatively correlated with area and age. Therefore, a taxon cycle that slows with island age appears to be a suitable concept to understand the dynamic nature and biodiversity patterns of Pacific Islands.

Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China. However, the majority region it covers in eastern China was an arid area during the Paleogene. The temporal history and essential factors involved in the evolution of subtropical EBLFs in eastern China remain enigmatic. Here we report on the niche evolution of Quercus section Cyclobalanopsis, that appeared in south China and Japan during the Eocene and became a dominant component of subtropical EBLFs since the Miocene in eastern Asia, using integrative analysis of occurrences, climate data and a dated phylogeny of 35 species in Cyclobalanopsis. Species within clades Cyclobalanoides, Lamellosa, and Helferiana mainly habitat in the Himalaya-Hengduan Region, adapting to a plateau climate, while species within the other clades mainly live in eastern China under the control of the East Asian monsoon. Reconstructed history showed that significant divergence of climatic tolerance in Cyclobalanopsis began around 19 Mya in the early Miocene. Simultaneously, the disparity in precipitation of wettest/warmest quarter and annal precipitation were remarkably enhanced in Cyclobalanopsis, especially in the recent eastern clades. During the Miocene, the remarkable radiation of Cyclobalanopsis and many other dominant taxa of subtropical EBLFs strongly suggest the rapid formation and expansion of subtropical EBLFs in eastern China. Our research highlights that the intensification of the East Asian monsoon and subsequent occupation of new niches by the ancient clades already present in the south may have jointly promoted the formation of subtropical EBLFs in eastern China since the early Miocene.

Pseudo-nitzschia is a group of wide-distributed planktonic diatoms. Some species produce the neurotoxin domoic acid (DA). Herein, two new Pseudo-nitzschia species were described from Chinese coastal waters and South China Sea after combining morphological and molecular data, together with biogeographical traits. Pseudo-nitzschia punctionis sp. nov. was similar to P. bipertita morphologically, but differed in poroid structure which was undivided in P. punctionis but divided in two sectors in P. bipertita. This difference corresponded to the presence of two HCBCs in ITS2 secondary structure. Pseudo-nitzschia polymorpha sp. nov. was sister to P. limii phylogenetically, but distinct by the various shapes of perforations on the valve and copula, which was supported by four HCBCs. In a metabarcoding analysis, multiple new ribotypes were identified within the two new species, and intra-specific genetic divergences were analyzed. Metabarcoding data revealed that P. punctionis had a broader temperature range (12.9-30.5℃) than P. polymorpha (22.3-30.5℃). Within the two new species, different traits were found among the ASVs regarding to the temperature and biogeography, representing different microevolutionary directions under environmental selection. The two new species had different biogeographical traits when compared to their closely-related species. Domoic acid was detected in strains of P. punctionis at a concentration of 13.5-17.7 fg cell^-1, but the toxin was not found in strains of P. polymorpha. A combination of characters based on laboratory strains and field metabarcoding data provided more data for delimiting Pseudo-nitzschia species and gave new insights on their diversity and biogeography.

Evolutionary theory suggests the hypothesis that among genetically isolated populations, phenotypic variation should be smaller in populations with smaller ratios of nonsynonymous to synonymous substitutions (dN/dS) because smaller dN/dS ratios occur under greater purification selections. Two distinct lineages (JPN1 and JPN2) of panarctic Daphnia pulex, invaded independently into Japan from North America, provide an excellent opportunity to test this hypothesis because the earlier invader JPN1 has a lower dN/dS ratio than JPN2. Therefore, we examined phenotypic variations in fitness-related traits, including digestive, life-history and morphological traits, among several genotypes within these two lineages. We found that phenotypic variations were smaller within the JPN1 lineage than within the JPN2 lineage. Furthermore, within-lineage variation of the phenotypic plasticity to changing food levels was smaller in the JPN1 lineage than in the JPN2 lineage. These results support the hypothesis that the JPN1 lineage has been more efficiently subjected to negative selection. However, the magnitude of the phenotypic plasticity of these traits was, on average, at the same level between the JPN1 and JPN2 lineages and its direction differed among genotypes of these lineages, suggesting that the JPN2 genotypes may have exploited niches that were different from those of the JPN1 genotypes.

Scots pine (Pinus sylvestris L) is one of the most important tree species of the temperate and boreal zones in Eurasia. Its wide distribution range and current patterns of genetic variation have been influenced by Quaternary climatic oscillations and the demographic processes connected to them. In order to better understand the relationship between evolutionary history and demographic factors in a widespread species with a large genome, we used SNP array to genotype thousands of single nucleotide polymorphism markers across 62 natural populations (N = 686 trees) of Scots pine in Eurasia. This provides the largest range-wide SNPs genetic diversity assessment of Scots pine to date. Our findings show evidence of past admixture events between genetic clusters that were retained despite the potential for effective pollen mediated gene flow across the species' distribution range. We also examined the contemporary population structure of the species and analyzed the range-wide genetic diversity patterns. Phylogenetic analyses and demographic modeling suggest that the observed divergence patterns between genetic lineages likely predate the last glaciation events. Two of the most distinctive groups are represented by trees from the eastern parts of Fennoscandia and Eastern Russia, which have remained separated since the mid-Pleistocene. The patterns of genetic variation also confirm the dual colonization of Fennoscandia and the existence of an admixture zone in Central Europe that was formed during multiple waves of postglacial recolonization. This study provides insights into the genetic relationships of Scots pine populations from Europe and Asia and offers a more comprehensive understanding of the species' history.

Newly investigated leafy twigs bearing axillary fruits from the Eocene Parachute Creek Member of the Green River Formation in eastern Utah, USA, have provided more information on the species previously attributed to the Proteaceae as Banksia comptonifolia R.W.Br. The leaves are simple, estipulate with short petioles and elongate laminae with prominent angular nonglandular teeth. The laminae have a thick midvein and pinnate craspedodromous secondaries, and are distinctive in the presence of a thick, often coalified, marginal rim. Vegetative and reproductive buds occur in the axils of the leaves. These features indicate that the species belongs to Palibinia Korovin--an extinct Eudicot genus previously known only from the Paleogene of Asia and Europe. Small pedicellate ovoid fruits 1.5–2.2 mm wide are borne in fascicles of three and are seen to be capsules with four apical valves. Despite the specific epithet referring to similarity of the foliage to that of Comptonia (Myricaceae), the fasciculate inflorescence organization with axillary flowers is quite distinct from the catkins characteristic of that family. Assignment to Banksia or other Proteaceae with complex inflorescences and follicular fruits is also problematic. Additionally, MacGinitie's transfer of the species to Vauquelinia of the Rosaceae is contradicted by the lack of stipule scars on the twig and by differences in leaf venation and floral morphology. We transfer the species to Palibinia comptonifolia (R.W.Br.) comb. nov., but its familial affinity within the Pentapetalae remains uncertain. This new occurrence augments records from the Paleogene of Turkmenistan, Kazakhstan, China, England, and Germany.

Phylogenetics is crucial in the study of evolutionary processes and events transpiring in the course of species diversification. Phylogenetic studies within kingdom Plantae often reveal hybridization and introgression. Here, we study a subsection rife with historic hybridization and discuss the impacts of such processes on evolutionary trajectories. Aliciella subsection Subnuda comprises seven species of herbaceous plants occurring in Utah, the Navajo Nation, and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of nuclear ITS and chloroplast DNA regions and genome-wide RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from the chloroplast and nuclear ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny and multispecies coalescent species tree robustly resolve relationships between six species-level clades. We employ STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest hybridization has occurred among all species in the subsection at some point in their history. Cytonuclear discordance reveals historic chloroplast capture, and we discuss potential causes of the observed discordance. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

A fundamental question in speciation genomics is how evolutionary processes shape the genomic landscape of differentiation between species. Regions of elevated differentiation, referred to as genomic islands, could be shared among closely related species (shared islands) or specific to a lineage (lineage-specific islands). Shared islands are typically assumed to result from background selection. However, simulations and empirical studies have suggested that positive selection contributes to both shared and lineage-specific islands. Here, we utilized comparative population genomics to examine the contributions of different evolutionary processes to patterns of genetic differentiation when gene flow and incomplete lineage sorting are minimal. We employed whole-genome resequencing data for 135 individuals from four oak species, including two independent species pairs, Quercus variabilis and Quercus acutissima in the subgenus Cerris, and Quercus dentata and Quercus griffithii in the subgenus Quercus. We found that both shared and subgenus-specific islands were caused by positive selection, including selective sweeps in current populations and in their most recent common ancestors. Moreover, the recombination rate was a better predictor of genomic differentiation than gene density. Overall, our results reveal that recombination and positive selection impacted genomic differentiation considerably and provide a more precise grasp of how genomic islands formed in Quercus.

Crassulaceae is a mid-sized family in angiosperms, most species of which are herbaceous succulents, usually with five-merous flowers and one or two whorls of stamens. Although previous phylogenetic studies revealed seven major ‘clades’ in Crassulaceae and greatly improved our understanding of the evolutionary history of the family, relationships among major clades are still contentious. In addition, the biogeographic origin and evolution of important morphological characters delimiting infrafamilial taxa have not been subject to formal biogeographic and character evolution analyses based on a well-supported phylogeny backbone. In this study, we used plastomic data of 52 species, representing all major clades revealed in previous studies to reconstruct a robust phylogeny of Crassulaceae, based on which we unraveled the spatiotemporal framework of diversification of the family. We found that the family may originate in southern Africa and then dispersed to the Mediterranean, from there to eastern Asia, Macaronesia and North America. The crown age of Crassulaceae was dated at ca. 63.93 million years ago (Mya), shortly after the Cretaceous-Paleogene (K-Pg) boundary. We also traced the evolution of six important morphological characters previously used to delimit infrafamilial taxa, and demonstrated widespread parallel and convergent evolution of both vegetative (life form and phyllotaxis) and floral characters (number of stamen whorls, petals free or fused, and flower merism). Our results provide a robust backbone phylogeny as a foundation for further investigations, and also some important new insights into biogeography and evolution of the family Crassulaceae.

We represent a comparative analysis of GBSS1 gene fragment sequences for a number of species related to Elymus caninus: E. prokudinii, E. viridiglumis, E. goloskokovii, as well as a number of morphologically deviating biotypes, inhabiting Russia and Kazakhstan. Microevolutionary relationships between species were assessed from dendrograms derived from sequences of exons and introns. In all taxa St subgenome was represented by St₂ variants, rather typical of the North American ancestral line of Pseudoroegneria spicata than of the Asian line descending from P. strigosa. All putative relatives of E. caninus had H₁ subgenome variants linked around the Asian diploid carrier of the H genome from Hordeum jubatum, and were divided into two subclades. One of them (H_1-1) contained most of closely related to E. caninus clones, including E. uralensis. Another subclade (H_1-2) consisted of five variants phylogenetically related to E. mutabilis. We have also studied reproductive relationships between species E. goloskokovii, E. prokudinii, and E. viridiglumis and a degree of their integration into the E. caninus complex. Biotypes included in sexual hybridization formed a single recombination gene pool, within which slight differences in reproductive compatibility were observed. A comprehensive study of microevolutionary differentiation of taxa showed the expediency of taxonomic revision. The species mentioned should probably be relegated to infraspecific rank within Elymus caninus s. l.