Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.

All yellow Camellia plants in China are threatened, but their classification is contentious. Here, we performed a phylogenetic reconstruction based on nuclear double-digest restriction site-associated DNA sequencing (ddRAD), transcriptomes, nuclear ribosomal internal transcribed spacer (nrITS), and the small single-copy region of the chloroplast genome, in combination with morphological evidence to help resolve taxonomic ambiguity of those rare and threatened species. Conflicting relationships were derived from nuclear and chloroplast sequences. The strong hybridization/introgression signal detected suggests reticulate evolution mainly caused this discordance pattern. The nuclear-ddRAD and RNA-seq phylogenies fit better to the yellow camellias' morphology, providing a clear resolution for inferring their relationships in China. Based on present phylogenetic analyses and morphological characters, we propose these taxonomic suggestions: (i) Camellia petelotii and Camellia nitidissima are distinct species; (ii) Camellia ptilosperma, Camellia longruiensis, Camellia longgangensis, and C. longgangensis var. grandis are conspecific with Camellia flavida; (iii) Camellia multipetala and C. longgangensis var. patens are synonyms of Camellia quinqueloculosa, and C. quinqueloculosa should be recognized as an independent species; (iv) Camellia wumingensis should be formally recognized as an independent species; (v) Camellia longzhouensis is a synonym of Camellia chrysanthoides; (vi) Camellia xiashiensis and Camellia parvipetala should be treated as synonyms of Camellia micrantha; (vii) Camellia achrysantha is a good species; (viii) Camellia tunghinensis is an independent species; (ix) species status of Camellia huana is well-supported; and (x) Camellia pingguoensis var. terminals should be correctly identified to species level as Camellia terminalis. These results provide the basis for the recognition 20 yellow Camellia species in China.

Exploring the frequency and distribution pattern of polyploid species in geographic parameters is of significance in understanding the mechanisms of polyploid speciation and evolutionary drivers of biodiversity. We here explored polyploid and paleopolyploid incidence frequency in a scale of 100×100 km grids in China. We found 33% of angiosperm species are polyploidy in China, and 23% of polyploid speciation. Western China and eastern China showed a significantly different polyploid and paleopolyploid frequency, with an evolutionary cradle of polyploid angiosperms in the Qinghai-Tibetan plateau. Herbaceous species exhibited higher polyploid frequency but lower paleopolyploid frequency than woody species, indicating the former experienced more rapid differentiation and speciation than the latter. Our results indicate that western China is an evolutionary cradle for polyploid angiosperms where harsh environment facilitates the establishment and survival of polyploids, while polyploid lineages tend to rediploidize to be diploids with sufficient time in suitable environment.

Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies have clarified the most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 82 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto- nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances were most likely to stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.

Santolina is a clear example of a genus lying in an alpha-taxonomic status, with species accepted only based on qualitative morphological descriptions. In particular, taxonomic issues still need to be resolved for Santolina populations from southern France and north-eastern Spain, and so, we carried out an integrative taxonomic study involving morphometrics, cypsela morphometrics, niche overlap, and phylogenetic analysis based on six plastid markers (trnH-psbA, trnL-trnF, trnQ-rps16, rps15-ycf1, psbM-trnD, and trnS-trnG). Our results revealed that the current taxonomic circumscription is not adequate. In particular, the Santolina populations at the foothills of eastern Pyrenees, previously included in the variability of Santolina benthamiana, have to be considered as a distinct species, namely, Santolina intricata. In addition, despite their high phylogenetic relatedness, S. benthamiana s.str. and Santolina ericoides can still be considered as distinct species due to clear morphological and ecological differentiation. Finally, we demonstrated that three different subspecies can be recognized in Santolina decumbens, a species endemic to Provence. For one of these subspecies, due to its extremely restricted distribution range, conservation issues are pointed out.

Leaf water storage capacity and osmotic strength are important traits enabling species to adapt to environments that are often moisture limited. However, whether these drought tolerance traits are correlated with the species diversification rate (DR) of plant lineages is yet to be determined. In this study, we selected a species-rich genus (Primulina) of plants widely distributed in karst regions in which species frequently experience variable periods of drought. We measured water storage capacity-related traits (including leaf thickness and water content per mass) and saturated osmotic strength in the leaves of 58 Primulina species growing in a common garden. Subsequently, using phylogenetic methods, we examined the relationships between the rate of species diversification and the drought tolerance traits and between the species DR and evolutionary rates of these traits. We found that neither water storage capacity nor saturated osmotic strength showed significant relationships with the rate of species diversification. However, the evolutionary rate of saturated osmotic strength showed a significant correlation with the species DR, although no comparable significant relationship was detected regarding the evolutionary rate of water storage capacity. Our study indicates that the diversification among Primulina species has typically been accompanied by an extensive divergence of leaf osmotic strength but not a divergence in leaf water storage capacity. These findings will enhance our current understanding of how drought tolerance influences the diversification of plant species in karst regions.

Identifying the factors that cause reproductive isolation and their relative importance in species divergence is crucial to our understanding of speciation processes. In most species, natural selection is commonly considered to play a large role in driving speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 Populus adenopoda individuals, we explored the factors related to reproductive isolation of these two closely related species. The results showed that the two species diverged ~5-10 million years ago (Ma), when the Qinghai-Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid. In highly differentiated genomic regions, the relative divergence (F_ST) and absolute divergence (d_xy) were significantly higher than the genomic background, θπ and shared polymorphisms decreased whereas fixed differences increased, which indicated that natural selection played a key role in the reproductive isolation of the two species. In addition, we found several genes that were related to reproduction that may be involved in explaining the reproductive isolation. Using phylogenetic trees resolved from haplotype data of Populus tomentosa and P. adenopoda, the maternal origin of P. tomentosa from P. adenopoda was likely to be located in Hubei and Chongqing Provinces.

Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats, which can be tested using comparative phylogenetics. These lines of inquiry have been developed to include target capture sequencing, which can yield phylogenomic scale data from herbarium specimens. Here, we test the relationship between taxonomically important morphological characters in the moss genus Fissidens, using a 400- locus data set generated using a target-capture approach in tandem with a three-locus phylogeny generated using Sanger sequencing. Phylogenetic trees generated using ASTRAL and Bayesian inference were used to test the monophyly of subgenera/sections. These trees provide the basis for ancestral character state reconstructions and phylogenetic correlation analyses for five morphological characters and characters related to the moisture habitat, scored from the literature and by specimen inspection. Many of these characters exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border of the gametophyte) and habitat moisture niche breadth, which could be interpreted as the more extensive limbidium enabling species to survive across a wider variety of habitats. We also found correlations between costa anatomy, peristome morphology, and the limbidium, which could reflect the evolutionary recruitment of genetic networks from the gametophyte to the sporophyte phase. The correlation found between average habitat moisture and the sexual system indicates that dioicous and polyoicous species are more likely to be found in moist habitats and that these higher moisture levels could be particularly, reproductively advantageous to species with separate sexes.

Extensive C-to-U editing has been reported from plastid genomes (plastomes) and mitochondrial genomes (mitogenomes) of spikemoss. While “reverse” U-to-C editing was recorded in other seed-free plants such as hornworts, quillworts, and ferns, it was not observed in spikemosses. However, no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses. Here, we report thousands of C-to-U editing sites from plastomes and mitogenomes of two species: 1767 and 2394 edits in Selaginella remotifolia, and 4091 and 2786 edits in Selaginella nipponica, respectively. Comparative analyses revealed two different editing frequencies among plastomes, but one similar frequency in mitogenomes. The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity. The high guanine and cytosine (GC) content caused by GC-biased mutations in organelle genomes might be related to the absence of U-to-C editing in Selaginellaceae. Using RNA-seq and whole-genome data, we screened the pentatricopeptide repeat (PPR) family and discovered that the number of aspartic acid-tyrosine-tryptophan (DYW) domain-containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes. Consequently, we hypothesize that associated evolution among RNA editing, GC-biased mutation in organelle genomes, and the PPR protein family encoded in the nuclear genome, is probably triggered by the aberrant DNA repair system in Selaginellaceae. Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae, which would contribute to understanding the evolution of post-transcriptional modifications of organelle genomes in land plants.

Techniques of reduced-representation sequencing (RRS) have revolutionized ecological and evolutionary genomics studies. Precise establishment of orthologs is a critical challenge for RRS, especially when a reference genome is absent. The proportion of shared heterozygous sites across samples is an alternative criterion for filtering paralogs. In the prevailing pipeline for variant calling of RRS data - PYRAD/ IPYRAD, maxSH is an often overlooked parameter with implications to detecting and filtering paralogs according to shared heterozygosity. Using empirical genotyping by sequencing data of two primroses (Primula alpicola Stapf and Primula florindae Ward) and their putative hybrids, and extra data sets of Californian golden cup oaks, we explore the impact of maxSH on filtering paralogs and further downstream analyses. Our study sheds light on the simultaneous validity and risk of filtering paralogs using maxSH, and its significant effects on downstream analyses of outlier detection, population assignment, and demographic modeling, emphasizing the importance of attention to detail during bioinformatic processes. The mutual confirmation between results of population assignment and demographic modeling in this study suggested maxSH = 0.10 has a potentially excessive and asymmetrical effect on the removal of truly shared heterozygous sites as paralogs. These results indicate that hybridization origin hypotheses of putative hybrids represented by results with maxSH = 0.25 and 0.50 are more credible. In conclusion, we revealed the critical hazard of paralogs filtration according to sharing heterozygosity at first, so that we propose to use specific protocols, rather than maxSH, to filter potential paralogs for closely related lineages.

Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high-quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user-friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20-30 Ma and peaking at approximately 24 Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.

Economically significant bean pests of the genus Chauliops are species rich in the areas surrounding the Qinghai-Tibet Plateau and provide an excellent system for speciation studies. Here, an integrative taxonomic approach, employing morphological analyses, population genetic methods, and multiple molecular species delimitation methods, was used to clarify the taxonomy of Chauliops in East and Southeast Asia. Four new species (Chauliops parahorizontalis Li & Bu, sp. nov., Chauliops albida Li & Bu, sp. nov., Chauliops bicoloripes Li & Bu, sp. nov., and Chauliops paraconica Li & Bu, sp. nov.) were described, which increases the number of Chauliops species in this area from six to 10; a key for Chauliops species is also provided. Phylogenetic analysis and divergence time estimation revealed that Chauliops was divided into four clades: Clade A (Chauliops bisontula + [Chauliops horizontalis + C. parahorizontalis sp. nov.]), Clade B (C. albida sp. nov. and C. bicoloripes sp. nov.), Clade C (Chauliops quaternaria and Chauliops zhengi), and Clade D (Chauliops fallax + [Chauliops conica + C. paraconica sp. nov.]). Two species diversification events of Chauliops estimated to have occurred 7-1 million years ago (Ma) and 25-13 Ma were detected. These speciation events were consistent with the two historical uplift events of the Qinghai-Tibet Plateau, suggesting that orogeny might have provided opportunities for the diversification of Chauliops species on the southeastern margin of the Qinghai-Tibet Plateau. Our findings show that population genetic analyses can be used to delimit related species and that orogeny is a key driver of species diversification on the southeastern margin of the Qinghai-Tibet Plateau.