Table of Contents

01 September 2024, Volume 62 Issue 5
Cover illustration: Similar to Darwin’s finches, the phyllostomid bats, which belong to the family Phyllostomidae, are a classic example of adaptive radiation, with an exceptionally broad range of food sources including insects, blood, fruits, nectar, and even vertebrates. Yue et al. (843-857) provide genomic and functional evidence that divergent selection of genes related to taste, digestion, absorption, and metabolism played a crucial role in driving the extensive dietary diversification within the bat clade.
  
    Research Article
  • Yang Yue, Dahu Zou, Shilin Tian, Hengwu Jiao, and Huabin Zhao
    J Syst Evol. 2024, 62(5): 843-857.
    https://doi.org/10.1111/jse.13060
    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.
    Two carnivorous bat species, Vampyrum spectrum and Megaderma lyra, belonging to phylogenetically distant families, Megadermatidae and Phyllostomidae, respectively, exhibit distinct evolutionary paths toward a carnivorous diet. Comparative genomics provides evidence of molecular adaptations within genes associated with lipid digestion, absorption, and metabolism in these carnivorous bats, aligning with their preference for a high-fat diet. Additionally, the presence of low genetic diversity underscores the urgency of conservation efforts aimed at safeguarding carnivorous bat populations.
  • Review
  • Darya Khan, AJ Harris, Qamar U. Zaman, Hong-Xin Wang, Jun Wen, Jacob B. Landis, and Hua-Feng Wang
    J Syst Evol. 2024, 62(5): 858-875.
    https://doi.org/10.1111/jse.13042
    The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1438-1870 species within approximately 130 genera predominantly distributed from northern Canada to Patagonia. Four centers of diversity from Central and North America (Chihuahua, Puebla- Oaxaca, Sonora-Sinaloan, and Jalisco) and three centers of diversity from South America (Southern Central Andes, Caatinga, and Mara Atlantica) have played a pivotal role in disbursing cacti around the globe. Mexico is considered the richest area in cacti species with close to 563 species grouped into 50 genera. Approximately 118 species have been domesticated by Mesoamerican people as food crops and for ornamental purposes. Cacti inhabit a wide range of ecosystems and climate regions, ranging from tropical to subtropical and from arid to semiarid regions. Species belonging to the genus Opuntia are the major food crop producers in the family. Cacti have derived characteristics from familial synapomorphies within the Caryophyllales. Reproduction occurs through pollination facilitated by birds, bats, bees, and other insects. Climate variability, whether natural or human-induced 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.
    The upper figure is the fruit and flower of the cacti species. The figure below is a distribution map of major cacti food crops.
  • Research Articles
  • Zhi-Qiang Lu, Yong-Zhi Yang, and Jian-Quan Liu
    J Syst Evol. 2024, 62(5): 876-888.
    https://doi.org/10.1111/jse.13044
    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.
    By integrating morphological and genetic evidence, along with geographical distribution, four species (Carpinus viminea, Carpinus fargesii, Carpinus laxiflora, and Carpinus londoniana) were recognized within the C. vimineaC. laxifloraC. londoniana species complex. Species boundaries of the redefined four species differ significantly from previous taxonomic treatments. The hybrids between C. fargesii and C. londoniana produce morphological traits similar to C. viminea that may have led to difficulties in determining species boundaries and outlining distribution range of each species.
  • Yu‐Qian Niu, Yu‐Xin Zhang, Xin‐Feng Wang, Jun Wen, Zhen‐Hui Wang, Ji Yang, Yu‐Guo Wang, Wen‐Ju Zhang, Zhi‐Ping Song, and Lin‐Feng Li
    J Syst Evol. 2024, 62(5): 889-902.
    https://doi.org/10.1111/jse.13043
    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.
    We observed distinct phenotypes of shade-habitat woody Araliaceae species (Fatsia japonica), which was grown under five different natural microhabitats (sunlight, shade, sunfleck, deepshade, and stronglight) in nature. To further find out how the shade-habitat plants responded to distinct light conditions, we performed a common garden experiment for four shade-habitat and one sun-habitat woody species of the Araliaceae family under high light and low light conditions, respectively, in the greenhouse and measured phenotypic and transcriptomic features. Our study provides evolutionary and ecological perspectives on how the sun-habitat and shade-habitat woody species respond to shade and sunlight environments.
  • Si Xu, Lu Meng, and Ying Bao
    J Syst Evol. 2024, 62(5): 903-914.
    https://doi.org/10.1111/jse.13039
    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.
    Phylogenetic analysis revealed that plants rbcS1 and other non-rbcS1 genes originated from a common ancient duplication event that occurred at least in seed plants ancestor. Then, rbcS1 was retained in a few plant lineages, including Oryza. In addition, five OprbcS genes showed a spatiotemporal and tissue-specificity expression pattern. OprbcS1, OprbcS2OprbcS4, and OprbcS5 were prominently expressed in roots 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).
  • Heng-Ling Zhou, Lei Wang, Yun-Xia Yue, Zhi Luo, Shun-Jie Wang, Li-Guo Zhou, Li-Jun Luo, Hui Xia, and Ming Yan
    J Syst Evol. 2024, 62(5): 915-927.
    https://doi.org/10.1111/jse.13046
    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 upland and lowland rice ecotypes were adapted to agroecosystems with contrasting soil-nitrogen conditions. Upland and lowland ecotypes are independently differentiated within japonica and indica subspecies, resulting in rarely shared genetic bases and different appearances in the ability of NH4+/NO3uptake.
  • Yiran Xu, Yingcan Li, Huiqiao Hu, Hengwu Jiao, Huabin Zhao
    J Syst Evol. 2024, 62(5): 928-941.
    https://doi.org/10.1111/jse.13059
    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.
    Genes associated with taste, digestive system, and metabolism underlie the evolution of dietary diversification in New World leaf-nosed bats.
  • Michael D. Crisp, Bui Q. Minh, Bokyung Choi, Robert D. Edwards, James Hereward, Carsten Kulheim, Yen Po Lin, Karen Meusemann, Andrew H. Thornhill, Alicia Toon, and Lyn G. Cook
    J Syst Evol. 2024, 62(5): 942-962.
    https://doi.org/10.1111/jse.13047
    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.
    Eucalypts are currently placed in three genera. Traditionally, Eucalyptus was defined by the operculate perianth. When earlier phylogenies placed Angophora, which has free sepals and petals, within Eucalyptus as sister to the bloodwood clade, which has opercula, the bloodwoods were segregated into a new genus, Corymbia. Here, we present a new next generation sequencing phylogeny of 392 species-level eucalypt taxa using 101 targeted low-copy nuclear loci. We find that Angophora is actually nested inside Corymbia and is sister to the red bloodwoods (Corymbia s.s.). A supported clade comprising the rest of Corymbia (spotted gums, yellow-jacket bloodwoods, and ghost gums) is thus separated from the red bloodwoods and requires a new generic name, which we here describe formally as Blakella. This phylogeny reveals homoplasy in the perianth evolution of the eucalypts. Either free petals were lost in the common ancestor of eucalypts and regained in Angophora, or opercula originated independently in the other eucalypt lineages.
  • Ana M. Bossa‐Castro, Matheus Colli‐Silva, José R. Pirani, Barbara A. Whitlock, Laura T. Morales Mancera, Natalia Contreras‐Ortiz, Martha L. Cepeda‐Hernández, Federica Di Palma, Martha Vives, and James E. Richardson
    J Syst Evol. 2024, 62(5): 963-978.
    https://doi.org/10.1111/jse.13045
    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.
    In this study, we aimed to reconstruct the phylogeny of the Theobromateae tribe with as many species as possible using WRKY DNA sequence and morphological data from herbarium specimens. We characterize the evolutionary trajectory of morphological characters and provide a framework that permits the study of crop wild relatives and the evolution of key agronomic traits in cacao and its wild relatives.
  • Pablo Aguado‐Ramsay, Tamara Villaverde, Ricardo Garilleti, J. Gordon Burleigh, Stuart F. McDaniel, Maren Flagmeier, Jurgen Nieuwkoop, Arno van der Pluijm, Florian Hans, Francisco Lara, and Isabel Draper
    J Syst Evol. 2024, 62(5): 979-992.
    https://doi.org/10.1111/jse.13040
    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.
    An enigmatic moss with anomalous morphology has been found throughout Europe. After unsuccessful attempts to solve the problem of specimen identification by Sanger sequencing, we employed targeted enrichment using data generated from the GoFlag 408 flagellate land plant probe kit in order to unravel the identity of these specimens.
    Our results demonstrate that all of the enigmatic samples correspond to a single species, Lewinskya affinis s. str., and thus the anomalies appear to be specific to this particular moss species.
    Massive sequencing techniques open up new possibilities for organism identification, and this method has proven to be successful in the identification of problematic species.
  • Andrés A. Del Risco, Diego A. Chacón, Lucia Ángel, David A. García
    J Syst Evol. 2024, 62(5): 993-1008.
    https://doi.org/10.1111/jse.13053
    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 family level.
    Despite the abundance of phylogenetic studies published in the scientific literature, exploring a comprehensively assembled tree of life has been hampered by the overly scattered nature of information and the scarcity of visualization tools for large trees. Here, we synthetized a family-level tree of life with almost 7500 terminals by compiling over 1400 phylogenetic studies, which was time-calibrated by using DNA sequences and data from the fossil records for thousands of taxa, and by employing hundreds of secondary calibrations. We also developed a mobile app for smartphones to interactively explore the resulting tree, which includes time-proportional branch lengths and small illustrations of the represented organisms at the terminals. With this, we provide a useful, publicly available tool for exploring the interrelationships of the vast diversity of life on earth.
  • Roser Vilatersana, Juan Antonio Calleja, Sonia Herrando‐Moraira, Núria Garcia‐Jacas, and Alfonso Susanna
    J Syst Evol. 2024, 62(5): 1009-1024.
    https://doi.org/10.1111/jse.13057
    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.
    This study deals with the biogeography of a complex of genera used as a model for analyzing the evolution of the Irano-Turanian and Mediterranean floras: the CarthamusCarduncellus 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. (Carduncellus, Phonus, and Femeniasia) 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 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.
  • Hong‐Xin Wang, Diego F. Morales‐Briones, Jacob B. Landis, Jun Wen, and Hua‐Feng Wang
    J Syst Evol. 2024, 62(5): 1025-1036.
    https://doi.org/10.1111/jse.13036
    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.
    The morphology of Linnaeoideae is diverse. Maximum likelihood (ML) phylogenetic analyses of Linnaeoideae were inferred with IQ-TREE using the concatenated nuclear gene dataset. Support values displayed at the branches are ML bootstrap percentages/Bayesian posterior probabilities. *Nodes with support of 100/1.0.
  • Fang‐Dong Geng, Meng‐Fan Lei, Nai‐Yu Zhang, Yao‐Lei Fu, Hang Ye, Meng Dang, Xue‐Dong Zhang, Miao‐Qing Liu, Meng‐Di Li, Zhan‐Lin Liu, and Peng Zhao
    J Syst Evol. 2024, 62(5): 1037-1053.
    https://doi.org/10.1111/jse.13061
    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 divergence time within East Asian walnuts was about 35.98 Ma. At about 9.78 Ma, section Cardiocaryon was divided into the northern and southern clades, the dynamic histories of which were different in response to climatic fluctuations since the late Miocene. Moreover, the uplift of Qinghai–Tibetan Plateau (QTP) might have promoted the divergence of sect. Dioscaryon.
  • Ming‐Xia Xie, Xing‐Yue Hu, Qi‐Yang Wang, Zheng Ren, Yu‐Bo Liu, Mei‐Qing Yang, Xiao‐Ye Jin, Xiao‐Min Yang, Rui Wang, Chuan‐Chao Wang, and Jiang Huang
    J Syst Evol. 2024, 62(5): 1054-1067.
    https://doi.org/10.1111/jse.13056
    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.
    Fine-scale genetic structure among Sui and other reference populations. (A–C) Principal component analysis based on the coancestry matrix. (D, E) Individual-based pairwise coincidence matrix and phylogenetic tree.