Geographical range size is a fundamental ecological characteristic of a species, and the product of complex interactions of many factors in its history. Here, we investigate the causes of range size variation among 43 species of the woody plant genus Betula (birches), which each occupy areas of between one and 20 million square kilometers in the northern hemisphere. We find their distributions are more affected by temperature variables than by precipitation variables. The climatic niche breadth, median latitude, width of seed wings, degree of bark peeling, and ploidy of species all have significant impacts on range size variation, but number of leaf veins and life form do not. Many of these attributes, and range size itself, have a phylogenetic component and, once phylogeny is accounted for, ploidy no longer has a significant effect on range size, and climatic niche breadth is clearly the most important factor. Our results therefore support the niche-breadth hypothesis for range size variation and to a lesser extent also support the dispersal-ability hypothesis and Rapoport's rule that range size decreases toward the tropics. The climatic niche breadth of Betula species is likely to be a key attribute in their ability to avoid decline or extinction under climate change.

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.

We describe a new species of Ampelopsideae (Vitaceae), Nekemias mucronata sp. nov., from the Rupelian of Cervera (Spain) and revise another fossil species, Ampelopsis hibschii, originally described from Germany. Comparison with extant Ampelopsideae suggests that the North American species Nekemias arborea is most similar to Nekemias mucronata while the East Mediterranean Ampelopsis orientalis is the closest living relative of A. hibschii. Our review of fossil data indicates that, during the Eocene, four species of Ampelopsideae occurred in Eurasia, that is, N. mucronata in the Czech Republic, A. hibschii in Kazakhstan, and two fossil species in the Far East (Ampelopsis cercidifolia and Ampelopsis protoheterophylla). In the Oligocene, a new species, Ampelopsis schischkinii, appeared in Kazakhstan; meanwhile, N. mucronata spread eastwards and southwards, and A. hibschii mainly grew in Central Europe. In the late Oligocene, N. mucronata became a relict in the Iberian Peninsula and Nekemias might have persisted in Western Eurasia until the latest Miocene (“Ampelopsis” abkhasica). The last occurrence of A. hibschii was in the Middle Miocene in Bulgaria, probably a refuge of humid temperate taxa, along with Ampelopsis aff. cordata. Carpological remains suggest that this lineage persisted in Europe at least until the Pleistocene. Our data confirm previous notions of the North Atlantic and Bering land bridges being important dispersal routes for Ampelopsideae. However, such dispersion probably occurred during the Paleogene rather than the Neogene, as previously suggested. A single species of Ampelopsideae, A. orientalis, has survived in Western Eurasia, which appears to have been linked to a biome shift.

Tetradium, a genus within Rutaceae, comprises nine species found in Eastern and Southeastern Asia, distinguished by their opposite pinnate leaves and apocarpous or subapocarpous gynoecium with follicular fruits. While Hartley's 1981 monograph provided foundational insights, a comprehensive phylogenetic analysis of the genus is lacking. Using next-generation sequencing (NGS), this study aims to (i) establish an NGS molecular data set for Tetradium, (ii) elucidate interspecific relationships via the hybrid capture method and (iii) investigate the taxonomic status of Euodia meliifolia var. celebica. Our data set comprised 28 samples across nine species, sequenced using Illumina Miseq and Hiseq 4000 platforms, with downstream analyses conducted using the HybPhyloMaker pipeline and ASTRAL. Our findings revealed five main groups supported by both molecular and morphological data, highlighting changes in ovule number and seed functionality. Notably, the hybrid capture method proved invaluable for studying old herbarium specimens. Finally, taxonomic revisions were proposed, including the reclassification of E. meliifolia var. celebica as Tetradium celebicum, the fossil Euodia costata as Tetradium costatum, and the fossil Euodia lignata as Tetradium lignatum. An updated description for T. celebicum, supplemented by a specific identification key, is provided.

Fossil wood is one of the crucial proxies for understanding terrestrial vegetation composition and development in the Earth's 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. 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 Tree Analysis using New Technology, Xenoxylon appeared basal to Araucariaceae in the data set combining genes and xylological characters, whereas Xenoxylon is placed next to Podocarpaceae in the data set combining genes and biomolecular characters. To find a reliable systematic placement of Xenoxylon, a combined data set 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 daisy tribe Anthemideae Cass. is one of the largest and most diverse tribes within Asteraceae. We analyzed a data set including 61 out of 111 Anthemideae genera, and all but four of the 19 currently recognized subtribes (Inulantherinae, Lapidophorinae, Lonadinae, and Vogtiinae) using a targeted high-throughput sequencing approach, the first focused on the tribe. We followed different phylogenomic approaches, using nuclear and plastid data, as well as additional analytical methods to estimate divergence times and diversification rates, to unravel the evolutionary history and classification of this tribe. Our results reinforce the phylogenetic backbone of the Anthemideae advanced in previous studies and further reveal the possible occurrence of ancient hybridization events, plastid capture, and/or incomplete lineage sorting (ILS), suggesting that complex evolutionary processes have played an important role in the evolution of this tribe. The results also support the merging of subtribe Physmasperminae into Athanasiinae and subtribe Matricariinae into Anthemidinae and clarify previously unresolved relationships. Furthermore, the study provides additional insights into the biogeographic patterns within the tribe by identifying three main groups: the Southern African Grade, the Asian Clade, and the circum-Mediterranean Clade. These groups partially coincide with previously identified ones. Overall, this research provides a more detailed understanding of the Anthemideae tribe and improves its classification. The study also emphasizes the importance of phylogenomic approaches for deciphering the evolutionary dynamics of large and diverse plant lineages.

The wild rats in the genus Rattus represent a group of murids characterized by rapid lineage diversification but limited morphological variation. Within this genus, there are several commensal species with high invasive capacity, such as Rattus norvegicus and R. rattus, which pose a global threat. Investigating the mechanisms behind their adaptive evolution is of utmost importance. In this study, we conducted morphological study and whole-genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into morphological differentiation, as well as genomic divergence and gene flow using assembled mitochondrion genome and high-quality single nucleotide polymorphisms. Despite their morphological similarity and large overlap in morphospace, our analyses revealed significant genetic differentiation at the genomic level among Rattus species in China and adjacent regions. Specifically, intraspecific differentiation was observed in R. nitidus, R. norvegicus, and R. tanezumi, which may be related to habitat heterogeneity and geographic isolation. We hypothesize that as invasive rats expand their habitat, the diversification of ecological environments might lead to more environmentally adapted evolution and accelerated genetic differentiation. Furthermore, Dsuite and TreeMix analyses detected substantial introgression among different Rattus species, particularly evident between R. norvegicus and R. tanezumi. Strong gene flow signals suggest frequent hybridization events among these species, which may facilitate the acquisition of new environmental adaptability during their expansion into new territories. This study provides a preliminary analysis that serves as a foundation for a more comprehensive investigation into the rapid lineage diversification and adaptive introgression among Rattus species.

Oleaceae, a eudicot family with great species diversity, has attracted much attention from botanists because it contains many plants with important economic, medicinal, and ornamental values. However, the history of polyploidization and ancestral genome reshuffling of Oleaceae remains unclear. Here, we clarified an Oleaceae-common hexaploidization (OCH) event occurring at ~53–61 million years ago (Ma) common in all Oleaceae plants and an Oleaceae-recent tetraploidization (ORT) event occurring at ~18–21 Ma shared by the lineages of Syringa, Olea, Osmanthus, and Fraxinus. We found that high-frequency polyploidization events drove the frequency of gene loss in Oleaceae genomes and extended the size of regions containing adjacent gene loss, thereby promoting the degree of genome fragmentation. We revealed that biased fractionation between the OCH- and ORT-produced subgenomes is likely attributed to the origin of allopolyploidization in the OCH and ORT events. Significantly, through paleochromosome rearrangement comparisons, we proposed a "two-step" genome duplication model for OCH and determined the duplicated orders of OCH tripled genome. We reconstructed 11 protochromosomes of the most recent ancestral Oleaceae karyotype (AOK) and elucidated the trajectories of immense paleochromosome reorganization of Oleaceae species from ancestral eudicot karyotype. Notably, we tracked the diversification history of secondary metabolite synthesis genes in the Oleaceae and explored the effects of paleogenome evolution on specialized metabolite synthesis. Our findings provide new insights into the polyploidization and paleogenomic evolution of Oleaceae and have important scientific significance for understanding the genetic basis of species and secondary metabolic diversity in Oleaceae.

The orchid Dactylorhiza cantabrica H.A. Pedersen is a narrow endemic occurring in the western Cantabrian Mountains in northwest Spain. Previous allozyme and morphological studies suggest that it might have resulted from the hybridization of two widespread congeners: the triploid Dactylorhiza insularis and the diploid Dactylorhiza sambucina. However, this hypothesis has not been tested using multiple genetic markers necessary to analyze 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 frequency-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 have been 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.

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 long terminal repeats (LTRs) 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 disease 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 roost, 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.

The two invasive Reynoutria species, Reynoutria japonica var. japonica and Reynoutria sachalinensis, and their hybrid Reynoutria x bohemica are often misidentified by managers and nonspecialists. 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 4582 single-nucleotide polymorphisms (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 Reynoutria x bohemica were 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 challenges. 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.

Currently, a wide range of genomic techniques is available at a relatively affordable price. However, not all of them have been equally explored in bryophyte systematics. In the present study, we apply next-generation sequencing to identify samples that cannot be assigned to a taxon by morphological analysis or by Sanger sequencing methods. These samples correspond to a moss with an enigmatic morphology that has been found throughout Western Europe over the last two decades. They exhibit several anomalies in the gametophyte and, on the rare occasions that they appear, also in the sporophyte. The most significant alterations are related to the shape of the leaves. Morphologically, all specimens correspond to mosses of the genus Lewinskya, and the least modified samples are potentially attributable to the Lewinskya affinis complex. Specimen identifications were first attempted using up to seven molecular markers with no satisfactory results. Thus, we employed data generated from targeted enrichment using the GoFlag 408 flagellate land plant probe set to elucidate their identity. Our results demonstrate that all the enigmatic samples correspond to a single species, L. affinis s.str. This approach provided the necessary resolution to confidently identify these challenging samples and may be a powerful tool for similar cases, especially in bryophytes.

Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally, Eucalyptus was defined by its operculum, but when phylogenies placed Angophora, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. Yet, generic delimitation in the tribe Eucalypteae remains uncertain. Here, we address these problems using phylogenetic analysis with the largest molecular data set to date. We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multispecies coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among Arillastrum, Angophora, Eucalyptus, and Corymbia using Shimodaira's approximately unbiased test. Phylogenetic mapping was used to explore the evolution of perianth traits. Monophyly of Corymbia relative to Angophora was decisively rejected. All alternative relationships among the seven currently recognized Eucalypteae genera imply homoplasy in the evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades, except that the expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears to be a reversal to the plesiomorphic perianth structure. Here, we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations. We also define and name three sections within Blakella (Blakella sect. Blakella, Blakella sect. Naviculares, and Blakella sect. Maculatae), and two series within Blakella sect. Maculatae (Blakella ser. Maculatae and Blakella ser. Torellianae). Corymbia is reduced to the red bloodwoods.

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 Theobromateae 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 Theobromateae 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 data set 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.

Understanding the richness and diversification processes in the Mediterranean basin requires both knowledge of the current environmental complexity and 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.

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 nonphyllostomid 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 grasses are one of the most diverse plant families on Earth. However, their classification and evolutionary history are obscured by their pollen stenopalynous (similar) morphology. A combination of high-resolution imaging of pollen surface ornamentation and computational analysis has previously been proposed as a promising tool to classify grass taxonomic boundaries. In this study, we test this hypothesis by studying Poaceae pollen across the phylogeny from plants collected in northern South America and also from published literature across the globe. We assessed if morphotypes that we establish using descriptive terminology are supported by computational analysis, if they vary along six (a)biotic variables and vary across the phylogeny. Based on this analysis, we constructed a reference framework for pollen surface ornamentation morphotypes. Our results showed that there is a wide variation of grass pollen surface ornamentation. We identified nine new and confirmed six known morphotypes, establishing a data set for 223 species (243 individual plant specimens) that represent 11 subfamilies. Computational analysis showed that our morphotypes are well-supported by two quantitative features of pollen sculptural elements (size and density). The specific data set and mapping of the phylogeny confirmed that pollen morphological sculpture is unrelated to (a)biotic variables and is diverse across the phylogeny.

Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China. However, the majority of the 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, which 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 exist 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 million years ago (Ma) in the early Miocene. Simultaneously, disparities in precipitation of wettest/warmest quarter and annual precipitation were markedly enhanced in Cyclobalanopsis, especially in the recent eastern clades. During the Miocene, the marked 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.

European wild carnations (Dianthus) are represented by a high number of taxa organized in unresolved taxonomies. In particular, taxa belonging to the Dianthus virgineus L. complex in the Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations, which are vital to understand boundaries and relations among plant diversity groups. Here, we examine the phenotypic features of nuclear genome organization testing for species boundaries in this complex. We have studied the chromosome number, the total haploid length (THL), and the relative genome size (RGS) in 122 populations belonging to 25 out of 33 taxa of the complex. All the studied populations have 2n = 2x = 30 chromosomes, and the THL ranges from 14.09 to 20.71 μm. Genome size estimations support the absence of polyploidization events, but show a certain degree of variation (0.318–0.423 arbitrary units). The RGS variation is not in agreement with current taxonomic treatment, but rather shows a geographical pattern, with higher values in Sicily and Sardinia. No correlation between the THL and the RGS was detected, possibly due to the stable chromosome number and the small size of chromosomes. A number of evolutionary unique groups lower than the number of currently accepted taxa may be hypothesized.

Interspecific trait divergence may reflect adaptation and reproductive isolation, particularly after the rapid differentiation that may follow the colonization of new environments. Although new lineages are generally expected to be morphologically and ecologically similar to their ancestors, environmental forces can also drive adaptive differentiation along specific phenotypic axes. We used climate niche models and comparative analyses based on a previously inferred phylogeny to examine the history of ecological and morphological divergence of Neotropical firs (Abies Mill., Pinaceae), a group of conifers that have recently colonized and diversified in the mountains of Mexico and northern Central America. We inferred past secondary contact zones by comparing current and past climate niche projections and looked for evidence of recent interspecific gene flow using genomic data. Neotropical firs have similar niches to each other and show a strong phylogenetic signal for most evaluated morphological traits. Analyses based on individual variables suggested a random walk model of differentiation. However, early adaptation to tropical conditions is inferred in the ancestor of the southernmost firs, as all modern southern taxa are differentiated climatically from Abies concolor, the northernmost species. In addition, observed autapomorphic traits for soil properties and the number of resin ducts in needles are consistent with possible species-specific adaptations. Thus, a combination of nonadaptive and adaptive processes along different phenotypic axes, some related to the environment, likely operated after the southward migration of this plant lineage from North America and its subsequent radiation in the Neotropics.

Having a comprehensive understanding of genetic differentiation, responses to environmental change and demographic history is critical for genetic improvement and conservation efforts. Forest trees are an excellent resource for understanding population differentiation and adaptive genetic variation due to their ability to adapt to different climates and environments. Cephalotaxus oliveri is a relict conifer endemic to China. In this study, we generated transcriptome data and identified 17 728 high-quality single-nucleotide polymorphisms (SNPs) from 18 populations. We found significant negative correlations between expression diversity and nucleotide diversity within and among populations, suggesting that gene expression and nucleotide diversity have a reciprocal relationship when the species adapts to the environment. The analyses of population structure showed that C. oliveri displayed a striking genetic structure with four groups. BayeScEnv and RDA methods detected the signatures of local adaptation, and identified that 738 outlier SNPs were associated with precipitation, temperature and soil conditions across heterogeneous environmental conditions. Approximate Bayesian computation analyses showed that the first and second divergence occurred in the late Miocene (c. 10.075 million years ago [Ma]) and the middle Pleistocene transition (c. 0.815 Ma), respectively. Ecological niche modeling of C. oliveri revealed signs of westward expansion after the last glacial maximum, while it was predicted to experience significant range contractions in future climate change scenarios. Geographical factors and environmental factors in southern China have played a critical role in establishing the current genetic diversity and population structure of C. oliveri. This study provides an important reference for forest resource management and conservation for C. oliveri.

Full plastomes have recently proven to be a valuable data source for resolving recalcitrant phylogenetic relationships in the flowering plant family Bromeliaceae. The study of complete plastomes has additionally led to the discovery of new structural rearrangements and advanced our understanding of bromeliad plastome diversity and evolution. Here, we focus on the study of full plastomes of the bromeliad subfamily Hechtioideae to assess phylogenetic relationships, marker informativeness, and plastome structure and evolution. Using whole-genome sequencing data, we de novo assembled and annotated new plastid genomes of 19 Hechtioideae species plus one representative each from the Pitcairnioideae and Puyoideae subfamilies and compared them with four additional available plastomes from other bromeliad subfamilies. Our phylogenetic analysis using complete plastome sequences not only recovered the three currently recognized genera of Hechtioideae as monophyletic, strongly supporting Mesoamerantha as sister of Bakerantha and Hechtia, but also improved statistical support at different phylogenetic depths within the subfamily. We identified a set of highly informative loci, some of them explored for the first time in Hechtioideae. Structural rearrangements, including expansions and contractions of the inverted repeats, large inversions, and gene loss and potential pseudogenization were detected mainly within the genus Hechtia. Evolutionary trait rate shifts were associated with the size and guanine–cytosine content of the small single copy and inverted repeats.

The recent development of genetic methods has facilitated the identification of cryptic species across different groups of organisms, including plants. However, next-generation sequencing has rarely been used to study cryptic speciation in plants, especially in bryophytes, organisms with a dominant haploid life phase. The ability to capture variation across the whole genome makes this method an effective tool for distinguishing cryptic lineages. We have focused on the genetic structure of the moss Meesia triquetra along the Alps-to-Scandinavia transect. We detected the presence of the two genetically critically different lineages of M. triquetra in Europe. These lineages overlap in both morphological characters of the gametophyte and distribution ranges. However, they considerably differ in ecological preferences to groundwater pH. While lineage 1 occupied alkaline to subneutral fens, lineage 2 occurred in fens saturated with neutral to acidic water. We consider the entities cryptic species with respect to genetic and ecological differences but the absence of morphological features necessary for determining the entities. We hypothesize that fragmentation of the ancestral population of the moss in geographically isolated refugia differing in the commonness of acidic and alkaline substrates led to consequent long-term adaptation to different environmental conditions, then drove diversification in M. triquetra.

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 is 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 of 16 archipelagos in the tropical and subtropical South Pacific. We then evaluate whether the results support the taxon cycle as a plausible mechanism for these observations. We find that most species in the Pacific arrived less than 5 Mya 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 for understanding the dynamic nature and biodiversity patterns of the Pacific Islands.

Small islands represent a common feature in the Mediterranean and host a significant fraction of its biodiversity. However, the distribution of plant species richness across spatial scales—from local communities (alpha) to whole islands (gamma)—is largely unknown, and so is the influence of environmental, geographical, and topographical factors. By building upon classic biogeographic theory, we used the species–area relationship and about 4500 vegetation plots in 54 Central Mediterranean small islands to identify hotspots of plant species richness and the underlying spatial determinants across scales. To do so, we fitted and averaged eight species–area models on gamma and alpha richness against island area and plot size, respectively. Based on positive deviations from the fitted curves, we identified 12 islands as cross-scale hotspots. These islands encompassed around 70% of species and habitat richness, as well as almost 50% of the rarest species in the data set, while occupying less than 40% of the total island surface. By fitting generalized linear mixed models, we found that gamma richness was mainly explained by island area and was weakly related to mean annual temperature (positively) and annual precipitation (negatively). As for alpha richness, after accounting for the idiosyncratic effect of habitats and islands, plot size and gamma richness remained the only significant predictors, showing a positive relationship. This work contributes to the understanding of the patterns and drivers of plant diversity in Central Mediterranean small islands and outlines a useful methodology for the prioritization of conservation efforts.

Habitat stability is important for maintaining biodiversity by preventing species extinction, but this stability is being challenged by climate change. The tropical alpine ecosystem is currently one of the ecosystems most threatened by global warming, and the flora close to the permanent snow line is at high risk of extinction. The tropical alpine ecosystem, found in South and Central America, Malesia and Papuasia, Africa, and Hawaii, is of relatively young evolutionary age, and it has been exposed to changing climates since its origin, particularly during the Pleistocene. Estimating habitat loss and gain between the Last Glacial Maximum (LGM) and the present allows us to relate current biodiversity to past changes in climate and habitat stability. In order to do so, (i) we developed a unifying climate-based delimitation of tropical alpine regions across continents, and (ii) we used this delimitation to assess the degree of habitat stability, that is, the overlap of suitable areas between the LGM and the present, in different tropical alpine regions. Finally, we discuss the link between habitat stability and tropical alpine plant diversity. Our climate-based delimitation approach can be easily applied to other ecosystems using our developed code, facilitating macro-comparative studies of habitat dynamics through time.

The general dynamic model (GDM) of oceanic island biogeography 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 the 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 their 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 model (IISP), 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 toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.

The fern genus Didymoglossum (Hymenophyllaceae) is not so diverse in Africa with seven species at most. However, its local taxonomy is surprisingly still strongly debated, in particular within the Didymoglossum erosum complex interpreted either as a single polymorphic species or as a group of at least three distinct but morphologically very close taxa (D. erosum, Didymoglossum chamaedrys, and Didymoglossum benlii). Investigating these taxonomic issues and more generally the diversity of the genus in Africa and its origin, we conducted a complete anatomo–morphological analysis coupled with a molecular phylogenetic work based on rbcL. Our results support the recognition of all seven species, including Didymoglossum robinsonii that is likely distinct from the Neotropical Didymoglossum reptans to which the African populations were traditionally attributed. We here propose new characters and a novel key to distinguish the seven African species which also include Didymoglossum ballardianum, Didymoglossum lenormandii, and Didymoglossum liberiense. Once the taxonomy is clarified with respect to the distinct evolutionary lineages evidenced, the biogeographic history of the genus in Africa is discussed based on a divergence time estimation and the reconstruction of the ancestral geographic areas. These analyses reveal a Mesozoic (Cretaceous) vicariance event within Didymoglossum which is the second one hypothesized for the family Hymenophyllaceae.

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 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 use STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results suggest that 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.

The sclerophyllous syndrome is characterized by well-defined traits (evergreen coriaceous leaves, inconspicuous flowers, and fleshy fruits). It has been hypothesized that lineages displaying the sclerophyllous syndrome show lower speciation rates than non-sclerophyllous lineages after the establishment of the mediterranean climate. Daphne gnidium displays sclerophyllous traits and some differentiation into three subspecies (gnidium, mauritanica, maritima), but the spatio-temporal origin of this taxonomic group is unknown due to the lack of a time-calibrated phylogeny of the whole genus. Here, we inferred phylogenetic relationships and divergence times of Daphne (32 species, 238 samples) and other genera of Thymelaeaceae (16 genera, 38 species, 34 samples) using the internal transcribed spacer (ITS), which revealed that the current circumscription of Daphne is profoundly polyphyletic because some species are nested within the genera Wikstroemia and Edgeworthia. In contrast, D. gnidium formed a well-supported clade as recognized in taxonomic accounts (subgenus Spachia). We found morphological and phylogenetic support for Daphne mauritanica as a monophyletic lineage sister to D. gnidium. Divergence between D. gnidium and D. mauritanica appears to have predated the establishment of seasonally dry conditions, which supports a pre-mediterranean temporal origin of the lineage. A phylogeographical analysis within D. gnidium based on 66 nrDNA (ITS) and 84 cpDNA (rps16, trnV) sequences agreed with the low differentiation of the species in the Pleistocene despite its large distribution range. Altogether, D. gnidium illustrates one more example of the sclerophyllous syndrome with no speciation after the onset of the mediterranean climate.

The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the well-known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD-seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras. We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA. Finally, we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern. Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans-Beringian ancestral distribution of the clade Benthamidia in the mid-Oligocene, dispersal from Mexico to eastern United States in the mid-Miocene, and early diversification of the EA clade in SW China. Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade. Species delimitation analysis suggested 17 species in the clade Benthamidia, including all recognized subspecies. By integrating the results of molecular data with morphology, we proposed to retain the subspecies without changing their ranks. Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence.

National key protected wild plants (NKPWPs) are species with important conservation value based on genetics, ecology, culture, and/or scientific research, which are also confronted with serious threats. However, their geographical distribution patterns and conservation status remain unclear. In this study, we compiled 1032 species of NKPWPs. We measured the diversity to identify hotspots of NKPWPs based on species richness, weighted range size rarity and a complementarity-based analysis. Comparing the distribution and hotspots of NKPWPs with the coverage of Chinese nature reserves (NRs), we assessed conservation effectiveness and identified conservation gaps. The results identified 13 diversity hotspots; only 9.5% of them were covered by NRs with >30% of the grid cell area, and even 19.5% were not covered at all by NRs. Overall, 44.7% of NKPWPs were effectively protected by national NRs. Despite this success, 571 species in Yunnan, Guizhou, Sichuan, Chongqing, Guangxi, Guangdong, southern Hainan, Taiwan, and northern Xinjiang remain unprotected by NRs. The protected proportion of plants with first-level protection was lower than that of plants with second-level protection. The low overall proportion of protected hotspots indicates that the conservation outlook for NKPWPs is not optimistic. This study identifies priority conservation areas and conservation gaps and provides a scientific reference for the conservation of wild plants in China.

Macroalgae have been a key ecological component of marine ecosystems since the Proterozoic period and are common fossil forms in Cambrian Burgess Shale-type Lagerstätten. However, in most cases, it is difficult to place these early fossil algae into modern groups because little distinctive morphology is preserved. Here, we describe a new form of macroalgae, Qingjiangthallus cystocarpium gen. & sp. nov., from the Qingjiang biota of South China. The new taxon is represented by 546 specimens remarkably preserved with characteristics that allow a phylogenetic placement into crown groups of red algae. Centimeter-sized thalli resemble members of the extant Rhodymeniophycidae (a subclass of the class Florideophyceae), and hence suggest a florideophycean affinity, which indicates that ahnfeltiophycidaen and rhodymeniophycidaen algae may have diverged at least 518Ma, accordant with estimations of molecular studies. The presence of possible cystocarps on Qingjiangthallus thalli suggests that evolutionary innovation of a triphasic life cycle in red algae may have occurred no later than the Early Cambrian. The branching patterns and branch width of Qingjiangthallus are consistent with the coarsely dichotomously branched morphogroup, which was previously present in the Ediacaran, Ordovician, and afterward, but absent in the Cambrian.

Reconstructing mitochondrial genomes of angiosperms is extremely intricate due to frequent recombinations which give rise to varied sized in Dendrobium mitogenomes and their structural variations, even in most orchid species. In this study, we first sequenced two complete and five draft mitochondrial genomes of Dendrobium using next-generation and third-generation sequencing technologies. The mitochondrial genomes were 420 538-689 048 bp long, showing multipartite (multichromosomal) structures that consisted of variably sized circular or linear-mapping isoforms (chromosomes). The comparison of mitochondrial genomes showed frequent gene losses in Dendrobium species. To explore structure variations of mitochondrial genomes in vivo, we quantified copy numbers of five mitochondrial genes and DNA contents per mitochondrion. The gene copy numbers and the DNA contents showed extreme differences during Dendrobium development, suggesting dynamic structures of mitochondrial genomes. Furthermore, phylogenetic relationships of 97 accessions from 39 Dendrobium species were constructed based on 12 nuclear single-copy genes and 15 mitochondrial genes. We discovered obvious discordance between the nuclear and mitochondrial trees. Reticulate evolution was inferred from the species network analysis in Dendrobium. Our findings revealed the rapid structural evolution of Dendrobium mitochondrial genomes and the existence of hybridization events in Dendrobium species, which provided new insights into in vivo structural variations of plant mitochondrial genomes and the strong potential of mitochondrial genes in deciphering plant evolution history.

Melica (Poaceae) consist of about 92 species distributed across temperate regions of the world. Within section Dalycum, Melica ciliata sensu lato forms a taxonomic complex of several species and subspecies with clinal morphological variation causing conflicting identifications. To resolve taxonomic confusion, we used three complementary approaches, through molecular, morphological, and phytoecological analyses. The double-digest restriction-associated DNA markers significantly support the monophyly of three taxa: (i) the Mediterranean Melica magnolii, (ii) the Eurasian Melica transsilvanica subsp. transsilvanica, and (iii) the west-European M. ciliata subsp. glauca. This differentiation is corroborated by the analysis of 22 morphometric variables. Furthermore, phytoecological analysis of 221 floristic inventories revealed habitat distinctions among these taxa. Our approach of integrative taxonomy argues for a specific distinction for these three taxa, and we include a key to separate these forms. These new molecular data on the section Dalycum, subsection Ciliatae, call for further phylogenetic analyses including samples of M. ciliata subsp. ciliata and other East-Mediterranean and South African taxa.

Common potato (Solanum tuberosum L.) and its wild relatives belong to Solanum section Petota. This section's phylogeny and species delimitation are complicated due to various ploidy levels, high heterozygosity, and frequent interspecific hybridization. Compared to the nuclear genome, the plastid genome is more conserved, has a haploid nature, and has a lower nucleotide substitution rate, providing informative alternative insights into the phylogenetic study of section Petota. Here, we analyzed 343 potato plastid genomes from 53 wild and four cultivated species. The diversity of sequences and genomes was comprehensively analyzed. A total of 24 species were placed in a phylogenetic tree based on genomic data for the first time. Overall, our results not only confirmed most existing clades and species boundaries inferred by nuclear evidence but also provided some distinctive species clade belonging and the maternally inherited evidence supporting the hybrid origin of some species. Furthermore, the divergence times between the major potato clades were estimated. In addition, the species discriminatory power of universal barcodes, nuclear ribosomal DNA, and whole and partial plastid genomes and their combinations were thoroughly evaluated; the plastid genome performed best but had limited discriminatory power for all survey species (40%). Overall, our study provided not only new insights into phylogeny and DNA barcoding of potato but also provided valuable genetic data resources for further systematical research of Petota.

The tribe Sonerileae in tropical Africa and Madagascar is a morphologically diverse lineage that consists of 239 species in 10 genera. In this study, we present the first in-depth phylogenetic analysis of African Sonerileae to test monophyly of the currently recognized genera. Phylogenetic analyses were performed using sequence data from two nuclear (nrITS and nrETS) and three plastid loci (accD-psaI, ndhF and psbK-psbL). Sampling consisted of 140 accessions including 64 African, 27 Malagasy, 46 Asian, and three neotropical Sonerileae together with a broad outgroup sampling (105 spp.). Phylogenetic relationships were inferred using maximum likelihood and Bayesian inference approaches, and a careful reassessment of morphological characters was carried out. Our results neither support the monophyly of the Old World nor African Sonerileae. The monospecific African genus Benna is partially supported as sister to Phainantha, one of the basal neotropical lineages, while African and Malagasy Medinilla are nested among the SE Asian genera. Gravesia (116 spp.), the most species-rich and morphologically diverse genus in Madagascar, is recovered as monophyletic. The African genera of Sonerileae Calvoa, Dicellandra, and Preussiella form well-supported clades. In contrast, Amphiblemma (including Amphiblemma molle) and Cincinnobotrys s.l. (including Cincinnobotrys felicis) are not monophyletic. To accommodate the caulescent C. felicis we propose reinstatement of the monospecific genus Bourdaria. For the distinctive A. molle a new genus Mendelia is described. Calvoa hirsuta is designated here as the type of genus Calvoa, lectotypes are designated for Medinilla engleri and Veprecella lutea, and a neotype is designated for Preussiella kamerunensis.