Dietary specialization stands as a major factor in the study of adaptive evolution and the field of conservation biology among animals. Although bats show unparalleled dietary diversification among mammals, specialized carnivory remains relatively rare within this group. Consequently, our comprehension of the genetic and conservation aspects associated with this specific dietary niche in bats has largely remained uncharted. To investigate molecular adaptations and conservation genetics in carnivorous bats, we produced a new draft genome assembly for the carnivorous bat Vampyrum spectrum. Furthermore, we utilized this genome alongside another distantly related carnivorous bat Megaderma lyra, to conduct genome-wide comparative analyses with other bat species. Our findings unveil that genes linked to lipid metabolism exhibit signatures of positive selection and convergent molecular adaptation in the two divergent lineages of carnivorous bats. Intriguingly, we have uncovered that the evolution of dietary specialization in carnivorous bats is accompanied by molecular adaptations acting on genes in the peroxisome proliferator-activated receptors pathways, which are crucial in regulating plasma lipid metabolism and sustaining lipid homeostasis. Additionally, our genomic analyses also reveal low genetic diversity in both carnivorous bat species. This pattern is attributed to their continuously declining population sizes and low levels of heterozygosity, signaling their vulnerability and emphasizing the pressing need for conservation efforts. These genomic discoveries advance our understanding of genetic underpinnings of carnivory in bats and underscore substantial conservation concerns associated with carnivorous bat species.

The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1, 438–1, 870 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 threatens 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 their evolution, worldwide distribution, and the environmental factors impacting cultivation.

Both hybridization and intraspecific morphological variation across environmental gradients complicate species delineation. We aimed to discern both possibilities that may blur species boundaries in the Carpinus viminea–Carpinus laxiflora–Carpinus londoniana species complex. We conducted statistical analyses on 535 specimens encompassing the entire distribution of this species complex to identify phenotypic clusters. Additionally, we analyzed genetic divergence and probable hybridization between clusters using 76 individuals from 37 populations. Based on phenotypic and genetic clusters, we tentatively recognized four species: C. viminea,C. fargesii,C. laxiflora, and C. londoniana. Except for rare overlapping distributions between C. fargesii and C. londoniana, the redefined four species are mostly allopatric to each another based on their distributions. The morphological delimitation, species boundary and distribution of each species differ distinctly from past taxonomic treatments. For example, specimens previously identified under C. viminea, in fact, belong to three different species. Hybrids between C. fargesii and C. londoniana exhibit morphological traits similar to C. viminea, thereby contributing to difficulties in determining species boundaries and outlining species distributions. These findings suggest that local selection and geographical isolation may together have promoted both phenotypic and genetic divergences within this species complex. However, interspecific hybridization blurs species boundaries by producing hybrids with phenotypic similarity in addition to intraspecific variation. This study emphasizes the importance of statistical analyses of population-level morphological and genetic variations across major distributional ranges for an integrative delimitation of species boundaries and the identification of hybridization and hybrids.

Elucidating how plant species respond to variable light conditions is essential to understanding the ecological adaptation to heterogeneous environments. Plant performance and gene regulatory network underpinning the adaptation have been well documented in heliophytic species. However, it remains largely unclear how the sciophytic plants respond to distinct light conditions. We measured phenotypic and transcriptomic features of four sciophytic (Fatsia japonica,Metapanax delavayi,Heptapleurum arboricola, and Heptapleurum delavayi) and one heliophytic woody species (Tetrapanax papyrifer) of the Araliaceae family under distinct light conditions. Our phenotypic comparisons demonstrate that the four sciophytic species maintain similar photosynthesis efficiency between high light and low light conditions. However, a significantly decreased photosynthesis rate was observed under the low light conditions of the heliophytic species compared with the high light conditions. In addition, our leaf anatomical analyses revealed that, while all five species showed different anatomical structures under distinct light conditions, the sciophytic species possessed a lower degree of phenotypic plasticity relative to the heliophytic species. Further comparisons of the transcriptome profiling showed that differentially expressed genes identified in the five species were functionally related to photosynthesis, secondary metabolites, and other basic metabolisms. In particular, differential regulation of the photosynthesis-related and photomorphogenesis-related genes were potentially correlated with the phenotypic responses to the distinct light conditions of the five species. Our study provides evolutionary and ecological perspectives on how the heliophytic and sciophytic woody species respond to shade and sunlight environments.

Rubisco is assembled from large subunits (encoded by chloroplast gene rbcL) and small subunits (encoded by the nuclear rbcS multigene family), which are involved in the processes of carbon dioxide fixation in the Calvin cycle of photosynthesis. Although Rubisco has been studied in many plants, the evolutionary divergences among the different rbcS genes are still largely unknown. Here, using a rice closely related wild species,Oryza punctata Kotschy ex Steud, we investigated the differential properties of the rbcS genes in the species. We identified five rbcS genes (OprbcS1 through OprbcS5),OprbcS1 showed a different evolutionary pattern from the remaining four genes in terms of chromosome location, gene structure, and sequence homology. Phylogenetic analysis revealed that plant rbcS1 and other non-rbcS1 genes originated from a common ancient duplication event that occurred at least in seed plants ancestor. RbcS1 was then retained in a few plant lineages, including Oryza, whereas non-rbcS1 was mainly amplified in angiosperms. OprbcS1,OprbcS2–OprbcS4, and OprbcS5 were prominently expressed in stems and seeds, young leaves, and mature leaves, respectively. The yeast two-hybrid assay detected a significant decrease in the interaction between OprbcS1 and OprbcL compared to the other four pairs of proteins (OprbcS2–OprbcS5 and OprbcL). We propose that OprbcS1 might be assigned a divergent function that was predominantly specific to nonphotosynthetic organs, whereas OprbcS2–OprbcS5, having different affinity in the assembly process of Rubisco, might be subfunctionalized in photosynthetic organs. This study not only deepens our understanding of the fine assembly of Rubisco, but also sheds some light on future de novo domestication of wild rice.

The soil-nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH₄⁺) and dry fields (mainly in the form of nitrate, NO₃⁻), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE-related traits among rice landraces as well as the genetic differentiation between NUE-associated genes and quantitative trait loci (QTLs). The japonica upland and lowland rice ecotypes showed large differences in their NUE-related traits such as the absorption ability for NH₄⁺ and NO₃⁻. The indica upland and lowland rice exhibited similar performances when cultivated in solutions containing NH₄⁺ or NO₃⁻ or when planted in paddy or dry fields. However, the indica upland rice possessed a greater ability to absorb NO₃⁻. We identified 76 QTLs for 25 measured traits using genome-wide association analysis. The highly differentiated NUE-associated genes or QTLs between ecotypes were rarely shared by japonica and indica subspecies, indicating an independent genetic basis for their soil-nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil-nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the japonica and indica subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil-nitrogen conditions and have implications for the improvement of NUE.

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.

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.

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.

Since the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family-level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.

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 small subfamily Linnaeoideae of Caprifoliaceae exhibits a disjunct distribution in Eurasia and North America, including Mexico, with most taxa occurring in eastern Asia or Mexico and the monospecific Linnaea Gronov. ex L. having a circumboreal to north temperate distribution. We sampled 17 of the 20 species representing all Linnaeoideae genera and used nuclear (target enrichment) and complete plastome sequence data to reconstruct the phylogeny. Our results show strong topological conflicts between nuclear and plastid data, especially concerning Dipelta Maxim. and Diabelia Landrein, supporting hybridization events complicating the deep diversification. Nuclear data were used for divergence time estimation and ancestral area reconstruction. The divergence time between the Mexican Vesalea M. Martens & Galeotti and the Linnaea clade was dated to 39.5 Ma, with a 95% highest posterior density of 28.2 Ma (mid-Oligocene) to 45.2 Ma (mid-Eocene). Reconstructed ancestral areas support a widespread common ancestor of Linnaea plus Vesalea in Mexico and at least another area (eastern Asia, North America, or Europe). The biogeographic analysis, including fossils, supports the ancestral range of Linnaeoideae to be widespread in central and western China + Europe + Mexico, or eastern and northern Asia + central and western China + Mexico, or central and western China + North America + Mexico. The North Atlantic and/or the Bering land bridges may be important in the widespread distribution across continents in the Northern Hemisphere. Our study highlights the importance of utilizing fossils in biogeographic inferences andusing data from different genomes while reconstructing deep and shallow phylogenies of organisms.

East Asia constitutes one of the largest and most complex areas of plant diversity globally. This complexity is attributable to the geological history and climatic diversity of East Asia. However, controversy persists over the biogeographical hypotheses and different studies on this topic. The demographical complexity of temperate deciduous woody plants and heterogeneity of geological and climatic fluctuations in East Asia remain poorly understood. We aimed to assemble the chloroplast and nuclear genomes of 360 individuals from five walnut (Juglans) species in East Asia and comprehensively analyze the phylogenetic inference, genetic structure, population demographic, and selection pressure. The results showed that East Asian walnuts could be divided into two major groups, that is, section Juglans/Dioscaryon and sect. Cardiocaryon. Within sect. Cardiocaryon, the samples were categorized into the northern clade and southern clade, both of which were affected by Quaternary glaciation; however, the southern clade was affected to a lesser extent. The population expansion events observed in sect. Cardiocaryon and sect. Dioscaryon since the late Miocene indicated that Neogene climate cooling substantially affected the distribution of Tertiary relict plants in East Asia. Biogeographic analysis results showed that the uplift of the Qinghai–Tibetan Plateau (QTP) might have contributed to the divergence within sect. Dioscaryon. Our findings highlight the heterogeneity of climatic fluctuations in the northern and southern regions of East Asia during the late Neogene and Quaternary periods and suggest that the uplift of QTP could have facilitated the divergence of temperate deciduous woody plants.

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 four Sui populations using genome-wide single nucleotide polymorphisms arrays. We analyzed the data using principal component analysis, 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.