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  • Lian‐Sheng Xu, Zhu‐Qiu Song, Shu‐Yuan Liao, and You‐Sheng Chen
    J Syst Evol. 2024, 62(6): 1227-1237.
    https://doi.org/10.1111/jse.13066
    The Crepidinae are the largest subtribe of the Cichorieae (Asteraceae). Debate remains over the circumscription and phylogeny of this subtribe, mainly due to its complex morphology and the poor phylogenetic signal provided by traditional Sanger sequencing markers. In this study, a well-resolved phylogeny of the subtribe Crepidinae, consisting of seven highly supported clades, was obtained for the first time using nuclear data with a phylogenomics approach (Hyb-Seq). Using this phylogeny along with other evidence, we propose a new taxonomic framework for the Crepidinae with seven lines and 29 genera, which merges subtribe Chondrillinae with the Crepidinae. We also describe a new monotypic genus, Qineryangia, that is characterized by broad involucres, loose imbricate phyllaries with wavy margins, and thick pappus bristles.
    The authors obtain a well-resolved phylogeny of the subtribe Crepidinae, consisting of seven highly supported clades, for the first time using nuclear data with a phylogenomics approach (Hyb-Seq), describe a new monotypic genus, Qineryangia, that is characterized by broad involucres, loose imbricate phyllaries with wavy margins, and thick pappus bristles, and also propose a new taxonomic framework for the Crepidinae with seven lines and 29 genera, which merges subtribe Chondrillinae with the Crepidinae.
  • Ling-Jian Gui, Deng-Feng Xie, Chang Peng, Ting Ren, Li-Ying Yu, Song-Dong Zhou, Xing-Jin He
    J Syst Evol. 2025, 63(1): 72-84.
    https://doi.org/10.1111/jse.13028
    Tongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well-resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes (ndhC, ndhJ, and petG) related to photosynthesis appear to have undergone significant selective pressure. Through high-resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa. However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long-obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.
    Investigation of the alpine genus Tongoloa and its close relatives, using chloroplast and and nuclear ribosomal DNA revealed conflicts between the nuclear and chloroplast sequences, along with intriguing discrepancies between morphological and molecular evolution, offering new clues for the previously contentious classification of Tongoloa.
  • Li-Ying Luo, Gui-Hua Jin, Peng-Fei Ma, De-Zhu Li
    J Syst Evol. 2024, 62(4): 702-714.
    https://doi.org/10.1111/jse.13038
    Many examples of phenotypic modifications resulting from high-elevation adaptation have been documented, however, the underlying processes responsible for these modifications and whether the continuity of the adaptation process remain elusive, particularly in plants. The alpine plants distributed along wide elevational gradients provide an ideal system to address this question. Here, we collected transcriptomes from multiple tissues of three species with different elevations (~1500, ~2500, and ~3600 m in the Hengduan Mountains, Southwest China) in two genera Fargesia and Yushania of alpine bamboos, respectively, and conducted evolutionary and expressional analyses. Results showed that high-elevation adaptation emerged earlier in the evolutionary history of both genera and evolved continuously as the elevation increased. Moreover, convergence of genetic changes was observed in the two genera, with amounts of candidate genes responsible for high-elevation adaptation identified under positive selection. Overall, our study provides an empirical example and valuable genetic resource for further investigation of high-elevation adaptation in plants and sheds new light on how plants adapting to high-elevation environments in a biodiversity hotspot.
    This figure displays two points: (i) both genera of alpine bamboo (Fargesia and Yushania) have already experienced selection for genes showing signals of adaptation to the high elevation despite when distributed at relatively low elevations; and (ii) as the elevation increased, a growing number of new elevation-specific positively selected genes (PSGs) (genes identified to be positively selected exclusively at a certain elevational gradient) associated with high-elevation adaptation continued to emerge in both genera. Based on the results above, we obtained two significant outcomes: (i) the early appearance of high-elevation adaptation in bamboo evolutionary history; and (ii) the process of high-elevation adaptation and their underlying genetic changes were continuous as the elevational gradients increased in both alpine bamboo genera.
  • 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.
  • Ya-Nan Cao, Meng-Hao Wang, Hang Ran, Bin Tian, Lu-Xian Liu, Qing-Nan Wu, Yan-Yan Liu, Hong-Wei Wang, and Shan-Shan Zhu
    J Syst Evol. 2025, 63(1): 170-182.
    https://doi.org/10.1111/jse.13076
    Dipelta Maxim. (Caprifoliaceae) is a Tertiary relic genus endemic to China, which includes three extant species, Dipelta floribunda, Dipelta yunnanensis, and Dipelta elegans. Recent progress in the systematics and phylogeographics of Dipelta has greatly broadened our knowledge about its origin and evolution, however, conflicted phylogenetic relationships and divergence times have been reported and warrant further investigation. Here, we utilized chloroplast genomes and population-level genomic data restriction site-associated DNA-single nucleotide polymorphisms (RAD-SNPs) to evaluate the interspecific relationships, population genetic structure and demographic histories of this genus. Our results confirmed the sister relationship between D. elegans and the D. yunnanensisD. floribunda group, but with cyto-nuclear phylogenetic discordance observed in the latter. Coalescent simulations suggested that this discordance might be attributed to asymmetric “chloroplast capture” through introgressive hybridization between the two parapatric species. Our fossil-calibrated plastid chronogram of Dipsacales and the coalescent modeling based on nuclear RAD-SNPs simultaneously suggested that the three species of Dipelta diversified at the late Miocene, which may be related to the uplift of the eastern part of Qinghai–Tibet Plateau (QTP) and adjacent southwest China, and increasing Asian interior aridification since the late Miocene; while in the mid-Pleistocene, the climatic transition and continuous uplift of the QTP, triggered allopatric speciation via geographical isolation for D. floribunda and D. yunnanensis regardless of bidirectional gene flow. Based on both plastid and nuclear genome-scale data, our findings provide the most comprehensive and reliable phylogeny and evolutionary histories for Dipelta and enable further understanding of the origin and evolution of floristic endemisms of China.
    A genome-scale phylogenetic study of the Chinese endemic genus Dipelta using plastome and nuclear RAD-SNP data suggested the three extant Dipelta species diversified in the late Miocene, possibly related to the uplift of the eastern Qinghai–Tibet Plateau and southwest China, and the increasing Asian interior aridification.
  • Yun-Feng Li, Lian Luo, Yang Liu, Qiang He, Ning-Ning Yu, Naren Gaowa, Zhao-Qin Yi, Jun-Jie Wang, Wei Han, Tao Peng, Boon-Chuan Ho, Xiaolan He, Li Zhang, Zhi-Duan Chen, Yu Jia, Qing-Hua Wang
    J Syst Evol. 2024, 62(4): 577-588.
    https://doi.org/10.1111/jse.13063
    Bryophytes, a monophyletic group comprising three major lineages, diversified soon after the terrestrialization of land plants. However, their internal phylogenetic relationships remain controversial. In this study, we reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastid data set to date, including 549 taxa that represent almost all known orders and two-thirds of families. The strongly supported phylogenetic inference enabled us to propose in mosses seven newly segregated families, that is, Baldwiniellaceae, Calyptrochaetaceae, Ctenidiaceae, Herpetineuraceae, Isodrepaniaceae, Pseudotaxiphyllaceae, and Rozeaceae, and one reduced family, that is, Climaciaceae. We also transferred the liverwort family Calyculariaceae from Fossombroniales to Pelliales. Recent advancements in molecular phylogeny have revolutionized bryophyte classification, tending to be more fragmental. Hence, we further propose a revised familial classification system for bryophytes that includes 45 orders and 142 families in mosses, 23 orders and 85 families in liverworts, and five orders and five families in hornworts.
    Bryophytes are morphologically distinct and diverse in land plants, and their internal phylogenetic relationships remain controversial. We reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastome data set to date, including 549 taxa that represent almost all known orders and two-third families. Based on the plastid genomic phylogeny presented here and the recently published systems, we further propose a revised familial classification system for bryophytes that includes seven newly segregated families and one reduced family in mosses.
  • Hong Qian
    J Syst Evol. 2025, 63(1): 62-71.
    https://doi.org/10.1111/jse.13129
    For clades originating in warm climates, the tropical niche conservatism hypothesis predicts that current biological assemblages in colder or drier climates are expected to have lower phylogenetic diversity, and species in colder or drier climates are expected to be more closely related to each other (i.e., higher phylogenetic clustering). Liverworts are one of the oldest clades of extant land plants. They originated about 500 Ma during a warm (“greenhouse”) period and experienced multiple major cycles of warm and cold periods. Here, I test the tropical niche conservatism hypothesis using liverwort assemblages distributed along an elevational gradient crossing about 5000 m of elevation in the central Himalaya. I found that, in general, phylogenetic diversity and dispersion decrease with increasing elevation and thus with decreasing temperature, which is consistent with the tropical niche conservatism hypothesis. Phylogenetic diversity decreases with elevation monotonically, but phylogenetic dispersion decreases with elevation in a triphasic (zig-zag) pattern, which is generally consistent with the triphasic pattern found in angiosperms and polypod ferns along the same elevational gradient. Temperature-related variables explained approximately the same amount of the variation in phylogenetic diversity and dispersion as did precipitation-related variables, although mean annual temperature explained 9%−15% more variation than did annual precipitation. Climate extreme variables explained approximately the same amount of variation in phylogenetic diversity and dispersion as did climate seasonality variables.
    Exploring geographic patterns and climatic correlates of phylogenetic diversity and dispersion in liverwort assemblages along an elevational gradient in the central Himalaya shows that phylogenetic dispersion decreases with increasing elevation, thus giving a triphasic (zig-zag) pattern with decreasing temperature.
  • Meng-Hua Zhang, Ze-Long Nie, Regina A. Fairbanks, Jing Liu, Robert Literman, Gabriel Johnson, Sara Handy, Jun Wen
    J Syst Evol. 2025, 63(1): 99-114.
    https://doi.org/10.1111/jse.13138
    Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan-Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.
    Graphical summary: Panax originated outside the Himalayan-Hengduan Mountains but experienced extinctions promoted by global climate cooling, underwent numerous dispersals potentially aided by warming during the Miocene, and diversified there after colonization. At different periods in time, the Himalayan-Hengduan Mountains region served as either a sink or a source region for Panax diversification.
  • Dong-Mei Jin, Quan Yuan, Xi-Ling Dai, Gregor Kozlowski, Yi-Gang Song
    J Syst Evol. 2024, 62(4): 677-686.
    https://doi.org/10.1111/jse.13022
    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.
    Subtropical evergreen broad-leaved forest (EBLF) is the predominant vegetation type in eastern China, of which the evolutionary history remains enigmatic. Quercus section Cyclobalanopsis has been dominant component of subtropical EBLFs since the Miocene in eastern Asia. Here we report on the niche evolution of Quercus section Cyclobalanopsis, using integrative analysis of occurrences, climate data and a dated phylogeny of 35 species in Cyclobalanopsis. Species belong to clades Cyclobalanoides, Lamellosa, and Helferiana usually habitat in the Himalaya–Hengduan region, adapting to a plateau climate; while species belonging to Semiserrata, Acuta, Glauca, and Gilva mainly live in eastern China, under the control of the East Asian monsoon. The disparity of tolerance to precipitation of the wettest quarter in Cyclobalanopsis has been markedly enhanced since 19 Ma. Meanwhile, significant divergence of climatic tolerance to precipitation began around the early Miocene. Our research highlights that the intensification of the East Asian monsoon system and subsequent species diversification and 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.
  • Guo-Qing Wang, Rosa A. Scherson, Diego Vera, Yun-Hao Bai, Jun Wen, Lin-Yuan Guo, Alice C. Hughes, Hua-Feng Wang
    J Syst Evol. 2024, 62(4): 603-620.
    https://doi.org/10.1111/jse.13017
    Hainan Island has the most extensive and well-preserved tropical forests in China. With rapid economic development of Hainan, biodiversity is increasingly at risk. Determining the spatial patterns of plant diversity in Hainan and explaining the drivers behind plant diversity are important considerations in assessing and maximizing the effectiveness of national parks, such as the newly designated Hainan Rainforest National Park. We assessed phylogenetic diversity patterns, and species richness using 106,252 georeferenced specimen records and a molecular phylogeny of 3,792 native plant species. Based on phylogenetic range-weighted turnover metrics, we divided Hainan flora into four major floristic units. The Grade of Membership model was used to further verify the four units, and to understand their boundaries and the internal structure of each floristic unit. Finally, the best combination model was used to explore the driving mechanisms underlying the division. Our results reveal that central Hainan is the most important hotspot for plant endemism and diversity, followed by the southern area. Environmental energy is the main factor determining the spatial patterns of native plant diversity on the island, and accessibility has the greatest impact on native plant diversity among social factors. We explore patterns of spatial phylogenetics and biogeography to identify potential priorities for management and conservation drivers of plant diversity patterns across Hainan, to provide the basis for the effective protection of native plant diversity and the improvement of national parks of Hainan Island.
    Representative species of the four floristic units. The bold line on the map represents the boundaries of four floristic units as shown in Fig. 6. (i) Tropical coastal vegetation; (ii) Tropical rainforest; (iii) Tropical mountain rainforest. (iv) Tropical shrubland. Species morphological adaptations to different habitats, from southern forests and mountains to northern plantations and coastal wetland plants, can be observed.
  • 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.
  • Xiu-Yan Feng, Yi-Qing Gong, Khang Sinh Nguyen, Hiep Tien Nguyen, Yong-Bo Liu, Jian Liu, Xun Gong
    J Syst Evol. 2024, 62(4): 739-757.
    https://doi.org/10.1111/jse.13031
    Understanding the driving forces of speciation is a central question in evolutionary biology. Cycas bifida (Dyer) K. D. Hill and Cycas micholitzii Dyer are two morphologically similar Cycas (Cycadaceae) species with deeply pectinate megasporophylls and dichotomously divided leaflets. Geographically, they are isolated by the Red River Fault Zone (RRFZ), which acts as a biogeographical barrier for many Cycas species. In this study, we investigated the divergence, genetic diversity, genetic structure, and demographic history of C. bifida and C. micholitzii to uncover the speciation mechanisms for the two endangered species. Results revealed high historical gene flow but low contemporary gene flow between the two species, with a deep divergence occurring in the Late Miocene. The long-term geographical isolation and ecological niche differentiation were identified as important factors in driving the divergence of the two species, supported by significant isolation by distance testing, barrier analysis, and niche consistency detection. Geographical isolation by the RRFZ played a pivotal role in facilitating their divergence by constraining gene flow. Conservation genetic analyses indicated high genetic diversity within both species, coupled with disparate responses to Pleistocene climate fluctuations: C. micholitzii experienced population expansion, while C. bifida displayed a mild bottleneck effect. To ensure the protection and long-term sustainability of two threatened species, relevant conservation guidelines were proposed based on the assessment of their genetic diversity and structure. This study furnishes valuable insights into the mechanisms underpinning species divergence and delivers actionable recommendations for cycad conservation.
    Cycas bifida and Cycas micholitzii are two leaflets dichotomously divided Cycas species that have morphological similarities with deeply pectinate megasporophylls. Population genetics revealed that the two species had high genetic differentiation and occupied different niches with a deep divergence that occurred in the Late Miocene. The long-term geographical isolation and ecological niche differentiation were identified as important factors in driving the divergence of the two species. Subsequently, each species made its own response to the Pleistocene climate fluctuations: a weak bottleneck effect in C. bifida and a population expansion in C. micholitzii.
  • Dan Xie, Tian‐Xiang Chen, Hong Du, Hui Wu, Jin‐Hua Ran
    J Syst Evol. 2025, 63(2): 479-491.
    https://doi.org/10.1111/jse.13122
    Assessing sampling biases caused by nonrandom specimen collecting is crucial in systematics, biogeography, and conservation. Nevertheless, research on the collecting biases of vascular plants in China remains limited. Here, we investigated the collecting status of gymnosperms in China using 48 673 herbarium specimens representing 180 Chinese gymnosperm species. The spatial and temporal patterns, collector and determiner biases, and phylogenetic and taxon biases were studied to comprehend the collecting bias of gymnosperms in China during 1900–2021. Meanwhile, we assessed the inventory completeness of gymnosperms to identify collecting hotspots and coldspots. The results showed that gymnosperms predominantly inhabit mountainous areas in China. The historical collecting of gymnosperms in China can be divided into two distinct stages with four peaks of collecting activities. The distribution of collected or identified specimens per individual displays significant skewness, and the collecting of gymnosperms has the issues of overcollecting or undersampling. Inventory completeness remains deficient, and collecting intensity is weak in both northern China and the range of 22°–25° N in the southern region (i.e., central Yunnan, southern Guangxi, and eastern Guangdong). Additionally, observation of the spatial distribution reveals both hotspots and coldspots scattered across mountain regions, lacking clustering. This study revealed a highly polarized collecting pattern for gymnosperms in China. Consequently, we recommend optimizing collecting measures, targeted specimen collecting, and continuous dynamic monitoring of gymnosperms in future collecting efforts. These recommendations hold relevance not only for gymnosperms in China but also for other land plants worldwide.
    The collecting of gymnosperms in China reveals a highly polarized pattern in terms of spatial and temporal distribution, as well as certain biases in phylogenetics and taxonomy. Generally, both collecting hotspots and coldspots scatter across mountain regions, lacking clustering. (i) time lapse in collecting history; (ii) frequency of specimen collecting; (iii) phylogenetic bias; and (iv) collecting hotspots and coldspots.
  • Biao-Biao Niu, Qi-Xiang Zheng, Yang Liu, Nina Lundholm, Sing Tung Teng, Xu-Dan Lu, Rui-Wei Ran, Li Zhang, Yang Li
    J Syst Evol. 2024, 62(4): 621-636.
    https://doi.org/10.1111/jse.13016
    Pseudo-nitzschia is a group of widely distributed planktonic diatoms. Some species produce the neurotoxin domoic acid. Herein, two new Pseudo-nitzschia species were described from Chinese coastal waters and the South China Sea after combining morphological and molecular data, together with biogeographical traits. Pseudo-nitzschia punctionis sp. nov. was similar to Pseudo-nitzschia bipertita morphologically, but differed in poroid structure, which was undivided in P. punctionis but divided in two sectors in P. bipertita. This difference corresponded to the presence of two hemicompensatory base changes (HCBCs) in the secondary structure of internal transcribed spacer 2. Pseudo-nitzschia polymorpha sp. nov. was sister to Pseudo-nitzschia limii phylogenetically, but distinct by the various shapes of perforations on the valve and copula, which was supported by four HCBCs. In a metabarcoding analysis, multiple new ribotypes were identified within the two new species, and intraspecific genetic divergences were analyzed. Metabarcoding data revealed that P. punctionis had a broader temperature range (12.9–30.5°C) than P. polymorpha (22.3–30.5°C). Within the two new species, different traits were found among the amplicon sequence variants regarding temperature and biogeography, representing different microevolutionary directions under environmental selection. The two new species had different biogeographical traits when compared to their closely related species. Domoic acid was detected in strains of P. punctionis at a concentration of 13.5–17.7 fg/cell, but the toxin was not found in strains of P. polymorpha. A combination of characters based on laboratory strains and field metabarcoding data provided more data for delimiting Pseudo-nitzschia species and gave new insights into their diversity and biogeography.
    Two new Pseudo-nitzschia species were described based on morphology and molecular phylogeny. A metabarcoding analysis revealed different biogeographical and temperature characters between two new species and their closely related species, which help to define the Pseudo-nitzschia species.
  • Enzo Jugieau, Victor Talmot, Cybill Staentzel, Sandra Noir, and Laurent Hardion
    J Syst Evol. 2024, 62(6): 1218-1226.
    https://doi.org/10.1111/jse.13075
    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.
    The three invasive Reynoutria species, Reynoutria japonica var. japonica, Reynoutria sachalinensis, and their hybrid Reynoutria x bohemica, are often confused during environmental management and control actions. Using 4582 single-nucleotide polymorphisms from a RADseq analysis, 12 morphometric characters, and flow cytometry, we resolved the taxonomic identity and ploidy level of 26 populations from North-East France: only one octoploid genotype for R. japonica, different hexaploid genotypes for R. x bohemica, and two cytotypes, tetraploid and hexaploidy, for R. sachalinensis.
  • Ryan A. Folk, Aliasghar A. Maassoumi, Carolina M. Siniscalchi, Heather R. Kates, Douglas E. Soltis, Pamela S. Soltis, Michael B. Belitz, and Robert P. Guralnick
    J Syst Evol. 2024, 62(6): 1201-1217.
    https://doi.org/10.1111/jse.13077
    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.
    Phyloregionalization analysis of Astragalus. This analysis identifies areas of Earth characterized by distinctive assemblages of phylogenetic lineages, indicated by separate colors.
  • Xing-Hao Li, Ru-Fan Li, Fang-Jing Hu, Shuai Zheng, Fu-Qiang Rao, Rong An, Yong-Hong Li, and De-Guang Liu
    J Syst Evol. 2024, 62(6): 1137-1149.
    https://doi.org/10.1111/jse.13079
    The Cucujiformia, with remarkable morphological, ecological, and behavioral diversity, is the most evolutionarily successful group within Coleoptera. However, the phylogenetic relationships among superfamilies within Cucujiformia remain elusive. To address the issues, we conducted a transcriptome-based macro-evolutionary study of this lineage. We sequenced the genomes and transcriptomes of three species from the superfamily Curculionoidea (two from Curculionidae and one from Brentidae), and obtained a data set of more than 569 990 amino acid alignments from 143 species of Cucujiformia. With the most complete collection of whole genomes and transcriptomes so far, we compared the performance of different data matrices with universal-single-copy orthologs (USCO). The resultant trees based on different data sets were consistent for the majority of deep nodes. Two USCO amino acid matrices (i.e., USCO75 and USCO750-abs80) provided well-resolved topology. The analyses confirm that Cucujoidea sensu Robertson et al. 2015 is a nonmonophyletic group, consisting of Erotyloidea, Nitiduloidea, and Cucujoidea sensu Cai et al. 2022. Moreover, Erotyloidea is the early-diverging group, followed by the clade Nitiduloidea. The preferred topologies supported a “basal” split of Coccinelloidea from the remaining superfamilies, and Cleroidea formed the second splitting group. The following phylogeny was supported at the superfamily level in Cucujiformia: (Coccinelloidea, (Cleroidea, ((Lymexyloidea, Tenebrionoidea), (Erotyloidea, (Nitiduloidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))))). Our comprehensive analyses recovered well-resolved higher-level phylogenetic relationships within the Cucujiformia, providing a stable framework for comprehending its evolutionary history.
    Comprehensive phylogenetic analyses reveal new higher-level phylogenetic relationships among taxa in Cucujiformia, providing a stable framework for clarifying the evolutionary history of this diverse and successful group.
  • Sulin Wen, Xiaowei Cai, Kun Yang, Yi Hong, Fuhua Fan, Qian Wang, Bingxue Zhang, Qiandong Hou, Yuxing Leng, Guang Qiao, Xiaopeng Wen, Xiaohui Shen
    J Syst Evol. 2025, 63(2): 245-267.
    https://doi.org/10.1111/jse.13130
    Rhododendron is a significant plant genus, with over 600 identified species in China. The subgenus Hymenanthes holds the largest number of Rhododendron germplasms and showcases strong environmental adaptability. However, there remains a lack of understanding regarding Rhododendron's evolution and environmental adaptations. Rhododendron bailiense Y.P.Ma, C.Q.Zhang & D.F.Chamb., an exceedingly rare species, thrives in the alkaline karst landforms of Guizhou, southwest China, different from the typical growing environment of other Rhododendron species. In this study, we present a chromosome-level genome assembly of R. bailiense, revealing a genome size of 923.3 Mb, a contig N50 of 24.5 Mb, and a total of 47 567 predicted genes. An evolutionary analysis indicated that R. bailiense diverged from its ancestors prior to the other subgenus Hymenanthes rhododendrons, with the expanded and contracted genes being notably enriched in “stress response” and “growth,” respectively. Rhododendron bailiense is predominantly found on limestone soil in the mountains of Guizhou, with only two wild populations known. The genome of R. bailiense contained a high copy number of ankyrin repeat (ANK) and Ca2+-ATPase (CAP) genes, primarily involved in Ca2+ transport, shedding light on how R. bailiense copes with karst high-calcium stress. In contrast, the structures of the ANKs displayed unique characteristics, while the CAPs showed conservatism. The R. bailiense genome provides new insights into the adaptation and evolutionary history of Rhododendron plants in karst environments, potentially offering valuable information for adaptive breeding and ecological enhancement in such challenging settings.
    Rhododendron bailiense is an extremely rare species that grows in the alkaline karst landscape of Guizhou, China, and stands out from the typical growing environment of other Rhododendron species. We present a chromosome-level genome assembly of R. bailiense, showing a genome size of 923.3 Mb, a scaffold N50 of 61.8 Mb, and a total of 47 567 predicted genes. The genome contains high copy numbers of ankyrin repeat (ANK) genes and Ca2+-ATPase (CAP) genes, which are mainly involved in Ca2+ transport, indicating how R. bailiense responds to karst high-calcium stress.
  • Lee‐Ping Ang, Fabian Brambach, Salvatore Tomasello, Jun Wen, Marc S. Appelhans
    J Syst Evol. 2025, 63(2): 416-430.
    https://doi.org/10.1111/jse.13127
    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.
    The phylogeny of Tetradium containing nine species is presented. One of the nine species, Tetradium celebicum (Koord.) T.G.Hartley ex Brambach & Appelhans, which was previously named Euodia mellifolia var. celebica, is taxonomically and systematically revised.
  • 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.
  • Xin Wang, Jiang‐Bao Xia, Jun‐Hong Bai, Shuo Yin, Wei Wang, Da‐Wei Wang, Xin‐Xin Yi, and Sheng‐Hong Dai
    J Syst Evol. 2024, 62(6): 1150-1164.
    https://doi.org/10.1111/jse.13064
    As an important halophyte in the Yellow River Delta, the Amaranthaceae C3 Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high-quality chromosome-scale reference genome by combining high-throughput sequencing, PacBio single molecule real-time sequencing, and Hi-C sequencing techniques with a genome size of 445.10 Mb and contigs N50 of 2.94 Mb. Through the annotation of the S. salsa genome, 298.76 Mb of the repetitive sequences and 23 965 protein-coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole-genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9 Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′-O-malonyl-celosianin II were identified and purified in both phenotypes, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa.
    A total of four betacyanins including betanidin, celosianin II, amaranthin and 6'-O-malonyl-celosianin II were identified and purified in both phenotypes of Suaeda salsa, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype.
  • Kong-Yang Zhu, Zhi-Ping Zhang, Le Tao, Run-Qi Jiang, Wen-Bo Huang, Yong-Gang Sun, Hai-Feng He, Hui-Lin Fu, Hao Ma, Xiao-Min Yang, Jian-Xin Guo, Xin Jia, Chuan-Chao Wang
    J Syst Evol. 2024, 62(4): 785-793.
    https://doi.org/10.1111/jse.13029
    The West Liao River (WLR) and Yellow River (YR) basins are two major centers of millet farming in northern China. The result from flotation analyses and the spatial distribution of archeological sites indicate that two distinct survival strategies—agriculture and pastoralism were adopted in the southern and western regions of the WLR. Previous studies of ancient populations from the western area of the WLR suggested a correlation between a pastoral economy in the Bronze Age Upper Xiajiadian culture with a decreased genetic affinity with YR farmers. However, the population history of the southern WLR is unknown mainly due to the lack of ancient genetic data. Here we report the genomic data of an ancient individual from the Majiazishan site from the Late Bronze Age southern WLR region associated with Upper Xiajiadian culture. Unlike individuals from western WLR, this individual derived ancestry entirely from Late Neolithic YR farmers. We found a genetic substructure of the ancient human population of Upper Xiajiadian culture, which is consistent with the differences in the subsistence strategies of western and southern WLR. Climate deterioration led to different populations occupying the west and the south, respectively, in the WLR: the nomadic population from the Amur River (AR) in the west and the agricultural population from the YR in the south.
    A principal components analysis (PCA) with various East Asian groups was first performed to investigate the overall genetic structure of the WLR_BA_o2. In the PCA result, WLR_BA_o2 and other ancient individuals from the West Liao Region, projected between the Yellow River (YR) and Amur River (AR) groups. WLR_BA_o2 cluster with WLR_LN projected most close to the Late Neolithic to Iron Age YR groups (YR_LN and YR_LBIA), while WLR_MN and WLR_BA shifts toward the AR groups and WLR_BA_o fully cluster with AR groups.
  • Suellen M. Gales, Kristene T. Parsons, Ellen E. Biesack, Jonathan Ready, Raquel Siccha-Ramirez, Leonardo C. Rosa, Ricardo Rosa, Matheus M. Rotundo, Roger Bills, Alan Erik S. Rodrigues, Luis Fernando S. Rodrigues-Filho, Jan McDowell, João Bráullio L. Sales
    J Syst Evol. 2024, 62(4): 715-738.
    https://doi.org/10.1111/jse.13027
    Gymnurid rays are found in tropical, subtropical, and temperate regions around the world, where they are associated with sandy or muddy bottoms in coastal areas, being easily distinguished from other rays by the width of the disc. In recent years, the systematics of this family have been revised extensively. However, there has been no comprehensive molecular review of the family based on an adequate sample of species and localities, which may have obscured the presence of distinct evolutionary lineages. The present study was based on samples of 12 of the 13 valid species of the genus Gymnura, which were used for a multilocus reconstruction of the evolutionary history of the family Gymnuridae. Our results indicate the existence of several cryptic gymnurid lineages, within the species Gymnura micrura, Gymnura lessae, Gymnura altavela, and Gymnura poecilura. Also, we indicate that only half of the species that compose the genus are known, as well their conservation status. The analyses also indicate that the gymnurids originated during the Paleocene, with events of dispersal and vicariance occurring through the formation of oceanographic barriers, and species diversification peaking during the Oligocene and Miocene. The results of the present study reinforce the need for a comprehensive revision of the systematics of the family, in particular, the widely distributed species that are considered valid taxa, but may, in fact, represent different cryptic species. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation measures.
    Summary of the hidden diversity of the species inside Gymnura, with the main biogeographical events that shape its origin and diversification.
  • María J. Bena, Matias C. Baranzelli, Santiago M. Costas, Andrea Cosacov, María C. Acosta, Andrés Moreira-Muñoz, Alicia N. Sérsic
    J Syst Evol. 2024, 62(4): 758-774.
    https://doi.org/10.1111/jse.13023
    Geoclimatic events driving South American aridization have generated biota differentiation due to barriers and new environment formation. New environments allow species climatic niche evolution, or the geographical expansion of an existing one. Understanding the role these processes play may clarify the evolution of South American biota. Gomphrena L. ranges across almost all the continent's arid environments. We tested whether South American drylands are biogeographically connected through the Gran Chaco but, due to different aridity levels, lineage diversification could have also been associated with the evolution of climatic niches and morphological or physiological traits. With available data, we generated a dated phylogeny, estimated ancestral ranges, performed diversification analyses, reconstructed ancestral states of two characters, and examined if niches have changed between lineages. Results showed that Gomphrena diversified throughout the easternmost South American drylands ~15.4 Ma, and subsequently three independent clades colonized the western arid regions during the last Andean pulse, and after the marine transgressions (~4.8–0.4 Ma) via the Gran Chaco. The colonization implied an increase in the diversification rate of annuals over perennials and the progressive east–west differentiation of the occupied climatic niche. This diversification was influenced by C4 photosynthesis, which could have acted as a niche opener to conquer new environments after the Paranaean Sea withdrew. Spatiotemporal patterns found in Gomphrena suggest that geographical expansion and evolution of climatic niches played a common but decoupled role in promoting diversification. These results show that the Gran Chaco may have acted as a historical connection linking South American drylands.
    We tested whether South American dry and arid biomes are linked through the Gran Chaco but, due to the difference in the aridity level, lineage diversification could have been also associated with the evolution of climatic niches and morphological or physiological traits. Results showed that Gomphrena diversified throughout the easternmost South American drylands ~15.4 Ma, and that three independent clades subsequently colonized the western arid regions (~4.8–0.4 Ma) during the last Andean pulse, and after the last marine transgressions via the Gran Chaco. The colonization implied an increase in the rate of diversification of annual over perennial species and the progressive east–west differentiation of the occupied climatic niche. This diversification was influenced by C4 photosynthesis, which could have acted as a niche opener for the conquest of new environments after the Paranaean Sea withdrew and allowed colonization of the western drylands. Spatiotemporal patterns found in Gomphrena suggest that geographical expansion and the evolution of climatic niches played a common but decoupled role in promoting diversification. These results show that the Gran Chaco may have acted as a historical connection generating a link between dry and arid South American regions.
  • Ning Liu, Xin‐Lai Wu, Ruo‐Bing Zhang, Jin Wang, Qi‐Sen Yang, Ji‐Long Cheng, Zhi‐Xin Wen, Lin Xia, Alexei V. Abramov, De‐Yan Ge
    J Syst Evol. 2025, 63(2): 307-318.
    https://doi.org/10.1111/jse.13123
    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.
    We performed whole-genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into genomic divergence and gene flow, utilizing assembled mitochondrial genomes and high-quality single nucleotide polymorphisms. Our analyses unveiled significant genetic differentiation at the genomic level among Rattus species in China and neighboring areas. Gene flow analyses detected substantial introgression signals among different Rattus species, with a particularly pronounced occurrence of gene flow between R. norvegicus and R. tanezumi. This study provides an initial analysis for a comprehensive exploration of rapid lineage diversification and adaptive introgression among Rattus species, serving as a foundation for further research.
  • Fang‐Pu Liu, Meng‐Qi Han, Peng‐Wei Li, Yin‐Zheng Wang
    J Syst Evol. 2025, 63(2): 401-415.
    https://doi.org/10.1111/jse.13124
    The genus Didymocarpus Wall. is a core group of the subfamily Didymocarpoideae in Gesneriaceae with a complex taxonomic history. It has long been controversial to delimit Didymocarpus and its allies. We conducted phylogenetic reconstructions with high-density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (external transcribed spacer [ETS], internal transcribed spacer [ITS], 18S, 26S) and five chloroplast DNAs (atpB-rbcL, rpl16, rps16, trnH-psbA, and trnL-F). The results indicated that neither Didymocarpus nor Allocheilos are monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitated the range of the Didymocarpus sensu stricto (s. str.) with two-section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution, in that it is found only in Southeast China. In addition, we proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera.
    We conducted phylogenetic reconstructions with high-density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (ETS, ITS, 18S, and 26S) and five chloroplast DNAs (atpB-rbcL, rpl16, rps16, trnH-psbA, and trnL-F). The results indicate that neither Didymocarpus nor Allocheilos are monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitate the range of the Didymocarpus sensu stricto (s. str.) with two-section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution, found only in Southeast China. In addition, we also proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera.
  • Eliise Kara, Jérémie Bardin, Dario De Franceschi, Cédric Del Rio
    J Syst Evol. 2024, 62(4): 809-828.
    https://doi.org/10.1111/jse.13033
    Menispermaceae are an angiosperm family of mostly climbing plants distributed throughout tropical regions. The fruits in this family have a strong sclerified endocarp and can be used for reliable species-level identifications, even in a fossilized form. New Paleocene-age menispermaceous endocarps have recently been discovered in South America and Asia, while in Europe, they are mostly found in the Eocene. This paper focuses on the study of fossil endocarps belonging to Menispermaceae, found in the Petit-Pâtis locality, which is one of the few Paleocene localities in Europe. The locality is dated to the late Paleocene (57–56 Ma) and the fossils represent flora and fauna in the Paris Basin before the onset of the Paleocene–Eocene Thermal Maximum. Lignitized fossils were photographed and their morphology was analyzed using computed tomography, scanning electron microscope, and geometric morphometric analysis. The analysis of 36 fossils belonging to Menispermaceae revealed that three genera (Stephania, Palaeosinomenium, Tinospora) were present in the late Paleocene of Paris Basin. Differences in internal morphology and a more inflated endocarp base led to a description of a new fossil species—Palaeosinomenium oisensis sp. nov. The occurrence of these genera in the Paleocene of France is consistent with the suggestion that megathermal flora was present in the Paris Basin before the Paleocene–Eocene Thermal Maximum. These three genera are currently the oldest occurrences in Europe, highlighting the connection between paleofloras of the Americas, Europe, and Asia in the Paleocene.
    This paper focuses on the study of fossil endocarps belonging to Menispermaceae, found in the Petit-Pâtis locality, which is one of the few Paleocene localities in Europe. Three genera (Stephania, Palaeosinomenium, Tinospora) and one new fossil species (Palaeosinomenium oisensis) are recognized in the Late Paleocene of Paris Basin before the onset of the Paleocene–Eocene Thermal Maximum. These three genera are currently the oldest occurrences in Europe, highlighting the connection between paleofloras of the Americas, Europe, and Asia in the Paleocene.
  • Yi Xiong, Yan-Li Xiong, Xue-Jie Jia, Jun-Ming Zhao, Li-Jun Yan, Li-Na Sha, Lin Liu, Qing-Qing Yu, Xiong Lei, Shi-Qie Bai, Xiao Ma
    J Syst Evol. 2024, 62(4): 794-808.
    https://doi.org/10.1111/jse.13020
    Quaternary glacial climate oscillation and geographical isolation have significantly influenced the geographic distribution pattern and lineage evolution history of species. However, understanding how these factors specifically impact the genealogical structure of dominant Gramineous species in the Qinghai–Tibet Plateau (QTP) remains a subject of investigation. Elymus sibiricus L. (Gramineae), indigenous to the QTP and widely distributed in Eurasia, exhibits remarkable environmental adaptation and phenotypic diversity, making it an ideal candidate for phylogeographic studies. Based on the analysis of 175 complete chloroplast genome sequences, our results indicated that the ancestors of E. sibiricus originated from the QTP and underwent a complex migration history. After the speciation of E. sibiricus, several geo-groups exhibited independent differentiation, showing minimal gene flow among them. The current phylogeographic patterns of E. sibiricus are a result of frequent climate alternations and the cold climate during the Quaternary glacial, as well as the presence of several geographical barriers that have restricted the gene flow among different geo-groups. Our research has revealed for the first time that E. sibiricus has a multilineage origin, and its maternal donors are not limited to a single species. Furthermore, the high quality and mapping depth of the variant file provided reliable data for analyzing the patterns based on raw sequencing data. These findings enhance our understanding of the relationship between plant differentiation and climatic and geographical factors of Eurasia.
    Characterization of the pan-chloroplast genomes of Elymus sibiricus endemic to Qinghai–Tibet Plateau (QTP) was performed. Ancestors of E. sibiricus (with the genome constitution of StStHH) from different origins may be different, and the St genome is of multiline origin. Elymus sibiricus originated from the QTP and underwent a complex migration process during the Quaternary ice age.
  • Jacopo Franzoni, Giovanni Astuti, Gianluigi Bacchetta, Giulio Barone, Fabrizio Bartolucci, Liliana Bernardo, Angelino Carta, Fabio Conti, Gianniantonio Domina, Božo Frajman, Gianpietro Giusso del Galdo, Duilio Iamonico, Mauro Iberite, Luigi Minuto, Marco Sarigu, Ana Terlević, Alessia Turini, Lucia Varaldo, Daniel Volgger, Lorenzo Peruzzi
    J Syst Evol. 2024, 62(4): 589-602.
    https://doi.org/10.1111/jse.13025
    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.
    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. Here, we examined phenotypic features of nuclear genome organization testing for species boundaries in this complex. A constant diploid chromosome number, coupled with few relative genome size (RGS) differences, was observed among taxa of the D. virgineus complex in the Central Mediterranean. A geographical, rather than taxonomic, RGS variation allowed speculations on the actual evolutionary relationships within this complex.
  • 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.
  • Oyetola Oyebanji, Gregory W. Stull, Rong Zhang, Fabien R. Rahaingoson, De-Zhu Li, and Ting-Shuang Yi
    J Syst Evol. 2024, 62(6): 1103-1117.
    https://doi.org/10.1111/jse.13072
    The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time-calibrated phylogeny for 749 species representing c. 80% of the genera of this clade using nrDNA ITS, plastid matK, and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade's temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil-calibrated dating analysis showed a nearly simultaneous divergence between the stem node (c. 62 Ma) and the crown node (c. 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c. 10 Ma. Possible explanations for the present-day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra- and intercontinental long-distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid-Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.
    In this study, we used chloroplast and nuclear data to reconstruct the phylogeny and to explore the evolutionary history of the Millettioid/Phaseoloid clade. The clade was estimated to originate in Africa during the early Paleocene (c. 62 Ma), followed by gradual accumulation of lineages through time, but with a sudden increase in net diversification rates from the late Miocene (c. 10 Ma) to the present. We observed 11 shifts in diversification rate across the phylogeny, reflecting a complex and heterogeneous evolutionary history. The global disjunct distributions of the clade were established via geodispersal and long-distance dispersal.
  • Jia-Xuan Mi, Jin-Liang Huang, Yu-Jie Shi, Fei-Fei Tian, Jing Li, Fan-Yu Meng, Fang He, Yu Zhong, Han-Bo Yang, Fan Zhang, Liang-Hua Chen, and Xue-Qin Wan
    J Syst Evol. 2025, 63(1): 160-169.
    https://doi.org/10.1111/jse.13074
    Taxonomy of Populus is a challenging task, especially in regions with complex topography, such as the Qinghai–Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the Flora of China, Populus pseudoglanca and Populus wuana are classified into sect. Leucoides and sect. Tacamahaca, respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of Populus on the plateau, we found 31 taxa from the two sections. Through identification based on morphology and habitats, we confirmed that the “P. pseudoglanca” recorded in the Flora of Sichuan is not true P. pseudoglanca, while P. pseudoglanca and P. wuana recorded in the Flora of China may refer to the same species. By performing whole-genome re-sequencing of 150 individuals from the 31 taxa, we derived 2.28 million single nucleotide polymorphisms (SNPs). Further genetic and phylogenetic analyses demonstrated that the genetic structure of P. wuana is extremely consistent with P. pseudoglanca, and they all originate through the natural hybridization between Populus ciliata in sect. Leucoides and Populus curviserrata in sect. Tacamahaca. Our results suggested that P. wuana should be merged with P. pseudoglanca taxonomically. This study not only clarifies the taxonomic confusions related to P. pseudoglanca and P. wuana but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.
    Principal component analysis and clustering analysis that Populus pseudoglauca and Populus wuana are morphologically similar and genetic and phylogenetic analysis demonstrated that they have consistent genetic structures. Ideed, ABBA-BABA and HyDe analysis revealed that they both originated from the hybridization of Populus ciliata and Populus curviserrata.
  • Bowen Kong, Chungkun Shih, Dong Ren, and Yongjie Wang
    J Syst Evol. 2024, 62(6): 1193-1200.
    https://doi.org/10.1111/jse.13071
    Neuroptera, as a small relic group of Insecta undergoing a rapid species diversification during the Mesozoic Era, is known by diverse extinct endemic lineages preserved as impression fossils and in amber. The current understanding of Mesozoic neuropterans' diversity has mainly focused on the adults, because the contemporaneous larvae have been fairly rare especially for the Jurassic lacewings. Herein, a new giant lacewing larva, Natator giganteus gen. et sp. nov., is described from the Middle Jurassic Daohugou Beds of China. The remarkable larva is characterized by its impressively large body size, distinctively elongated cervix, and presence of swimming hairs on legs, which provide direct evidence to reveal an aquatic habit for the Jurassic lacewing larva. The morphological analysis indicates this giant larva would have probably inhabited the benthic environments of Jurassic montane rivers and streams. In addition, its morphological specialization suggests that it might have adopted an ambush predation strategy to catch its prey. The finding enhances our knowledge of the species diversity and morphological plasticity for the Jurassic lacewing larvae, and reveals that the aquatic lineages of Neuroptera exhibited dramatically structural and ecological convergence across the evolutionary process.
    Describing a new giant lacewing larva, Natator giganteus gen. et sp. nov., from the Middle Jurassic Daohugou Beds of China. The larva′s impressive size, elongated cervix, and swimming hairs on legs offer direct evidence of its aquatic habit, suggesting this larva likely inhabiting benthic environments in Jurassic montane rivers and streams, adopting an ambush predation strategy. The finding enhanced our knowledge of the species diversity and morphological plasticity for the Jurassic lacewing larvae, and also revealed that the aquatic lineages of Neuroptera exhibited the dramatically structural and ecological convergence across the evolutionary process.
  • Raman Patel, Ashif Ali, Rafael F. de Almeida, Rajendra S. Rana, Mahasin A. Khan
    J Syst Evol. 2025, 63(2): 331-344.
    https://doi.org/10.1111/jse.13078
    Eucalypt fossils were widely reported from the Cenozoic deposits across the Southern Hemisphere (Australia, New Zealand, and Argentina). However, no attached reproductive and vegetative fossil remains of this myrtaceous clade have been discovered till now. We report and describe for the first time a fossil eucalypt twig with attached foliage, flower buds, and mature flowers from the early Eocene (~55–52 Ma) sediments (Palana Formation) of Rajasthan, western India. As both vegetative and reproductive organs are in organic connection, they clearly represent the same species. In addition, here we also introduce fossil materials of isolated leaves, flower buds, inflorescence, and flowers recovered from the same stratigraphic level. Our Eocene fossils and extant members of the eucalypt clade are related morphologically by means of robust, thick petiolate lanceolate-shaped leaves with intramarginal secondary veins; operculate flower buds consisting of imbricate petals with discernable margins; solitary inflorescence with three flowers per umbellaster, epigynous and bisexual flowers. Based upon combined characteristics of leaf, flower, and bud morphology, these fossils conform to the Eucalypt clade and are recognized as a new fossil genus and species: Hindeucalyptus eocenicus Patel, R.F. Almeida, Ali et Khan gen. nov. et sp. nov. We also compare it with extant and extinct eucalypts using morphological phylogeny and character mapping analyses. In addition, we briefly discuss its phytogeographic and paleoclimatic implications regarding the distribution and habitat of fossil and modern eucalypts.
    Herein, we report and describe for the first time the well-preserved fossilized eucalypt twig with attached foliage, flower buds, and free fuse inflorescence with flowers from the early Eocene (~55–52 Ma) sediments (Palana Formation) of Rajasthan, western India. Based upon combined characteristics of leaf, flower, and bud morphology, our Eocene fossil specimens are recognized as a new fossil genus and species Hindeucalyptus eocenicus sp. nov. We discuss its phytogeographic and paleoclimatic implications.
  • Xue Dong, Xiuxiu Zhu, Zechen Tang, Wenbo Yi, Huaijun Xue, Zhen Ye, Chenguang Zheng, Wenjun Bu
    J Syst Evol. 2025, 63(2): 345-358.
    https://doi.org/10.1111/jse.13120
    A full understanding of local adaptation at the genomic level will help to elucidate its role in the differentiation between closely related species. This study focused on rice seed bugs sister species (Leptocorisa chinensis and Leptocorisa oratoria), which are native to East Asia and are notorious pests targeting growing rice spikelets. East Asia is a region where diverse geology and fluctuating climate are known to have profound impacts on organisms. In this study, single nucleotide polymorphisms (SNPs) from double-digest restriction site-associated DNA sequencing and geographic distribution information were used to investigate phylogeography and assess the environmental contribution to genetic variation. We found clear genetic differentiation between sister species, but a lack of genetic structure within species because of their long-distance dispersal ability. The demographic model involved a scenario in which divergence in isolation (~0.6 Ma) was followed by secondary contact (~7 kya). The initial divergence may have been caused by the intensification of the East Asian monsoon during the Pleistocene climate oscillation. The historical demography indicated that the effective population size (Ne) showed an evident increase from 9 to 7 kya, which may be related to rice domestication and extensive human cultivation during the Holocene. We also detected a significant correlation between genetic and environmental distance, and the niche difference occupied between them. Temperature-related variables were ranked as the main factors for the difference, and 410 selective SNPs involved in adaptation were identified. The Nanling Mountains in southern China serve as a geographical boundary between them and act as an ecological barrier belt that promotes local environmental adaptation. Our study demonstrates that historical climate change and local adaptation by climate-imposed selection shape the phylogeographical patterns of sister species.
    We focused on the rice seed bugs sister species (Leptocorisa chinensis and Leptocorisa oratoria), notorious pests targeting growing rice spikelets native to East Asia. We combined double-digest restriction site-associated DNA sequencing and geographic distribution information to elucidate the phylogeographical pattern. There was significant isolation by environment; temperature-related variables were ranked as the main factors and selective single nucleotide polymorphisms involved in adaptation were identified. Both species, which are bounded by the Nanling Mountains in southern China, serve as an ecological barrier belt that promotes local environmental adaptation.
  • Yanjie Zhang, Conrad C. Labandeira, Jiamiao Yu, Chungkun Shih, Dong Ren, Taiping Gao
    J Syst Evol. 2025, 63(2): 359-368.
    https://doi.org/10.1111/jse.13121
    Based on several earwigfly specimens with well-preserved mouthparts of Meropeidae from mid-Cretaceous Burmese amber, a detailed, initial analysis was conducted of the structure of Mesozoic meropeids. Compared to the singularly flattened mandible of modern meropeids, the new specimens reveal that Mesozoic representatives had two distinct types of mandibles: blade-shaped and scoop-shaped. Current fossil evidence indicates that during the Mesozoic Era, Meropeidae displayed sexual dimorphism that was reflected in the structure of their mandibles. This structural difference may indicate that about 99 million years ago, meropeids had a more complex diet than extant confamilial taxa. Phylogenetic results suggest that Torvimerope gen. nov., along with Burmomerope, two extinct genera, form a clade and that are the sister taxon to crown-group Meropeidae. The new material offers new possibilities for inferring the feeding habits and mating behavior of early Meropeidae.
    Zhang et al. reported a trend in meropeids (Insecta, Mecoptera) toward shortening the rostrum, widening the clypeus, and reducing mandible size and teeth throughout their entire evolutionary process. These Cretaceous meropeids displayed sexual dimorphism, which was reflected in the structure of their mandibles, suggesting a more complex diet around 99 Ma.
  • Aixa Tosal, Alba Vicente, Thomas Denk
    J Syst Evol. 2025, 63(2): 379-400.
    https://doi.org/10.1111/jse.13126
    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 (“Ampelopsisabkhasica). 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.
    Synthesis of the paleobiogeographical history of Ampelopsideae from Eurasia. Nekemias mucronata sp. nov. (A); Ampelopsis hibschii (B). The results indicate that both species were already present in Eurasia during the late Eocene and later, during Oligocene times, dispersed across Eurasia. The last population of N. mucronata thrived in Spain during the late Oligocene while A. hibschii persisted in Bulgaria until the Middle Miocene. These data confirm the North Atlantic and Bering land bridges as key dispersal routes for Ampelopsideae. Nevertheless, this dispersion presumably occurred during the Paleogene rather than the Neogene, as previously suggested.
  • Qiang He, Yuqing Miao, Xinyuan Zheng, Yaru Wang, Yitao Wang, Zheng Jia, Hongyu Zhang, Yu Wang, Yao Xiao, Cailian Du, Wei Li, Longsheng Xing, and Huilong Du
    J Syst Evol. 2024, 62(6): 1085-1102.
    https://doi.org/10.1111/jse.13068
    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.
    In this study, we reported a near-complete genome assembly of Reynoutria multiflora and characterized its evolution in Polygonaceae. Combining transcriptomic and metabolomic analyses, we also revealed accumulation patterns and biosynthesis pathways of anthraquinone and stilbene in different growing years. Our results provide a valuable genomic resource for the comprehensive research of the biosynthesis of medicinal active ingredients and molecular breeding of R. multiflora.
  • Hua Yan, Peng Zhou, Wei Wang, Jian‐Fei Ye, Shao‐Lin Tan, Chun‐Ce Guo, Wen‐Gen Zhang, Zi‐Wei Zhu, Yi‐Zhen Liu, and Xiao‐Guo Xiang
    J Syst Evol. 2024, 62(6): 1165-1176.
    https://doi.org/10.1111/jse.13055
    Pterocarya (Juglandaceae) is disjunctly distributed in East Asia and the Caucasus region today, but its fossils are widely distributed in the Northern Hemisphere. We first inferred phylogeny with time estimation of Pterocarya under node-dating (ND) based on plastomes of all eight extant species and tip-dating (TD) based on plastomes and 69 morphological characters of 19 extant and extinct species, respectively. We compared the biogeographical reconstructions on the timetrees from ND and TD, respectively, and then compiled 83 fossil records and 599 current occurrences for predicting the potential distributions for the past and the future. The most recent comment ancestor of Pterocarya is inferred in East Asia at 40.46 Ma (95% highest posterior density [HPD]: 28.04–54.86) under TD and 26.81 Ma (95% HPD: 23.03–33.12) under ND. The current distribution was attributed to one dispersal and one vicariant event without fossils, but as many as six dispersal, six vicariant, and 11 local extinction events when considering fossils. Pterocarya migrated between East Asia and North America via the Bering Land Bridge during the early Oligocene and the early Miocene periods. With the closure of Turgai Strait, Pterocarya dispersed between East Asia and Europe through the Miocene. The potential distribution analyses indicated that Pterocarya preferred warm temperate regions across the Northern Hemisphere since the Oligocene, but the drastic temperature decline caused its extinction in high latitudes. Except for Pterocarya fraxinifolia and Pterocarya stenoptera, suitable habitats for this genus are predicted to contract by 2070 due to climate change.
    In this study, we summarized the fossil history of Pterocarya, and explored its biogeographical combined paleontological and plastid phylogenomic data. Our results showed that the modern distribution of Pterocarya was attributed to six dispersal, six vicariant, and 11 local extinct events with fossils, while it resulted from one dispersal and one vicariant event without fossils. Our results highlight the importance of integrating paleontological and phylogenetic data in understanding the geographical assembly of biodiversity through time.