Journal of Systematics and Evolution最新文献

{"title":"An integrative delimitation of the species' boundaries within one hornbeam species complex (Betulaceae: Carpinus)","authors":"Zhi-Qiang Lu, Yong-Zhi Yang, Jian-Quan Liu","doi":"10.1111/jse.13044","DOIUrl":"https://doi.org/10.1111/jse.13044","url":null,"abstract":"Both hybridization and intraspecific morphological variation across environmental gradients complicate species delineation. We aimed to discern both possibilities that may blur species boundaries in the <i>Carpinus viminea</i>–<i>Carpinus laxiflora</i>–<i>Carpinus londoniana</i> species complex. We conducted statistical analyses on 535 specimens encompassing the entire distribution of this species complex to identify phenotypic clusters. Additionally, we analyzed genetic divergence and probable hybridization between clusters using 76 individuals from 37 populations. Based on phenotypic and genetic clusters, we tentatively recognized four species: <i>C. viminea</i>, <i>C. fargesii</i>, <i>C. laxiflora</i>, and <i>C. londoniana</i>. Except for rare overlapping distributions between <i>C. fargesii</i> and <i>C. londoniana</i>, the redefined four species are mostly allopatric to each another based on their distributions. The morphological delimitation, species boundary and distribution of each species differ distinctly from past taxonomic treatments. For example, specimens previously identified under <i>C. viminea</i>, in fact, belong to three different species. Hybrids between <i>C. fargesii</i> and <i>C. londoniana</i> exhibit morphological traits similar to <i>C. viminea</i>, thereby contributing to difficulties in determining species boundaries and outlining species distributions. These findings suggest that local selection and geographical isolation may together have promoted both phenotypic and genetic divergences within this species complex. However, interspecific hybridization blurs species boundaries by producing hybrids with phenotypic similarity in addition to intraspecific variation. This study emphasizes the importance of statistical analyses of population-level morphological and genetic variations across major distributional ranges for an integrative delimitation of species boundaries and the identification of hybridization and hybrids.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"28 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139556069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ghost of past climate acting on present-day plant diversity: Lessons from a climate-based delimitation of the tropical alpine ecosystem","authors":"Martha Kandziora, Juan M. Gorospe, Luciana Salomon, Diana L. A. Vásquez, Maria Pinilla Vargas, Filip Kolář, Petr Sklenář, Roswitha Schmickl","doi":"10.1111/jse.13048","DOIUrl":"https://doi.org/10.1111/jse.13048","url":null,"abstract":"Habitat stability is important for maintaining biodiversity by preventing species extinction, but this stability is being challenged by climate change. The tropical alpine ecosystem is currently one of the ecosystems most threatened by global warming, and the flora close to the permanent snow line is at high risk of extinction. The tropical alpine ecosystem, found in South and Central America, Malesia and Papuasia, Africa, and Hawaii, is of relatively young evolutionary age, and it has been exposed to changing climates since its origin, particularly during the Pleistocene. Estimating habitat loss and gain between the Last Glacial Maximum (LGM) and the present allows us to relate current biodiversity to past changes in climate and habitat stability. In order to do so, (i) we developed a unifying climate-based delimitation of tropical alpine regions across continents, and (ii) we used this delimitation to assess the degree of habitat stability, that is, the overlap of suitable areas between the LGM and the present, in different tropical alpine regions. Finally, we discuss the link between habitat stability and tropical alpine plant diversity. Our climate-based delimitation approach can be easily applied to other ecosystems using our developed code, facilitating macro-comparative studies of habitat dynamics through time.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"34 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Perianth evolution and implications for generic delimitation in the eucalypts (Myrtaceae), including the description of the new genus, Blakella","authors":"Michael D. Crisp, Bui Q. Minh, Bokyung Choi, Robert D. Edwards, James Hereward, Carsten Kulheim, Yen Po Lin, Karen Meusemann, Andrew H. Thornhill, Alicia Toon, Lyn G. Cook","doi":"10.1111/jse.13047","DOIUrl":"https://doi.org/10.1111/jse.13047","url":null,"abstract":"Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally, <i>Eucalyptus</i> was defined by its operculum, but when phylogenies placed <i>Angophora</i>, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, <i>Corymbia</i>. Yet, generic delimitation in the tribe Eucalypteae remains uncertain. Here, we address these problems using phylogenetic analysis with the largest molecular data set to date. We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multispecies coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among <i>Arillastrum</i>, <i>Angophora</i>, <i>Eucalyptus</i>, and <i>Corymbia</i> using Shimodaira's approximately unbiased test. Phylogenetic mapping was used to explore the evolution of perianth traits. Monophyly of <i>Corymbia</i> relative to <i>Angophora</i> was decisively rejected. All alternative relationships among the seven currently recognized Eucalypteae genera imply homoplasy in the evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades, except that the expression of separate sepals and petals in <i>Angophora</i>, which is nested within the operculate genus <i>Corymbia</i>, appears to be a reversal to the plesiomorphic perianth structure. Here, we formally raise <i>Corymbia</i> subg. <i>Blakella</i> to genus rank and make the relevant new combinations. We also define and name three sections within <i>Blakella</i> (<i>Blakella</i> sect. <i>Blakella</i>, <i>Blakella</i> sect. <i>Naviculares</i>, and <i>Blakella</i> sect. <i>Maculatae</i>), and two series within <i>Blakella</i> sect. <i>Maculatae</i> (<i>Blakella</i> ser. <i>Maculatae</i> and <i>Blakella</i> ser. <i>Torellianae</i>). <i>Corymbia</i> is reduced to the red bloodwoods.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"1 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"List of Reviewers","authors":"","doi":"10.1111/jse.13051","DOIUrl":"https://doi.org/10.1111/jse.13051","url":null,"abstract":"","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"62 1","pages":"193-194"},"PeriodicalIF":0.0,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139480414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic and transcriptional features of Araliaceae species under distinct light environments","authors":"Y. Niu, Yu-Xin Zhang, Xinfeng Wang, Jun Wen, Zhen‐Hui Wang, Ji Yang, Yu‐Guo Wang, Wen‐Ju Zhang, Zhi‐Ping Song, Linfeng Li","doi":"10.1111/jse.13043","DOIUrl":"https://doi.org/10.1111/jse.13043","url":null,"abstract":"Elucidating how plant species respond to variable light conditions is essential to understanding the ecological adaptation to heterogeneous environments. Plant performance and gene regulatory network underpinning the adaptation have been well documented in heliophytic species. However, it remains largely unclear how the sciophytic plants respond to distinct light conditions. We measured phenotypic and transcriptomic features of four sciophytic (Fatsia japonica, Metapanax delavayi, Heptapleurum arboricola, and Heptapleurum delavayi) and one heliophytic woody species (Tetrapanax papyrifer) of the Araliaceae family under distinct light conditions. Our phenotypic comparisons demonstrate that the four sciophytic species maintain similar photosynthesis efficiency between high light and low light conditions. However, a significantly decreased photosynthesis rate was observed under the low light conditions of the heliophytic species compared with the high light conditions. In addition, our leaf anatomical analyses revealed that, while all five species showed different anatomical structures under distinct light conditions, the sciophytic species possessed a lower degree of phenotypic plasticity relative to the heliophytic species. Further comparisons of the transcriptome profiling showed that differentially expressed genes identified in the five species were functionally related to photosynthesis, secondary metabolites, and other basic metabolisms. In particular, differential regulation of the photosynthesis‐related and photomorphogenesis‐related genes were potentially correlated with the phenotypic responses to the distinct light conditions of the five species. Our study provides evolutionary and ecological perspectives on how the heliophytic and sciophytic woody species respond to shade and sunlight environments.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"32 14","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138949058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular evolution of the rbcS multiple gene family in Oryza punctata","authors":"Si Xu, Lu Meng, Ying Bao","doi":"10.1111/jse.13039","DOIUrl":"https://doi.org/10.1111/jse.13039","url":null,"abstract":"Rubisco is assembled from large subunits (encoded by chloroplast gene rbcL) and small subunits (encoded by the nuclear rbcS multigene family), which are involved in the processes of carbon dioxide fixation in the Calvin cycle of photosynthesis. Although Rubisco has been studied in many plants, the evolutionary divergences among the different rbcS genes are still largely unknown. Here, using a rice closely related wild species, Oryza punctata Kotschy ex Steud, we investigated the differential properties of the rbcS genes in the species. We identified five rbcS genes (OprbcS1 through OprbcS5), OprbcS1 showed a different evolutionary pattern from the remaining four genes in terms of chromosome location, gene structure, and sequence homology. Phylogenetic analysis revealed that plant rbcS1 and other non‐rbcS1 genes originated from a common ancient duplication event that occurred at least in seed plants ancestor. RbcS1 was then retained in a few plant lineages, including Oryza, whereas non‐rbcS1 was mainly amplified in angiosperms. OprbcS1, OprbcS2–OprbcS4, and OprbcS5 were prominently expressed in stems and seeds, young leaves, and mature leaves, respectively. The yeast two‐hybrid assay detected a significant decrease in the interaction between OprbcS1 and OprbcL compared to the other four pairs of proteins (OprbcS2–OprbcS5 and OprbcL). We propose that OprbcS1 might be assigned a divergent function that was predominantly specific to nonphotosynthetic organs, whereas OprbcS2–OprbcS5, having different affinity in the assembly process of Rubisco, might be subfunctionalized in photosynthetic organs. This study not only deepens our understanding of the fine assembly of Rubisco, but also sheds some light on future de novo domestication of wild rice.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"40 18","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138950081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seeking the identity of an enigmatic moss by embracing phylogenomics","authors":"Pablo Aguado‐Ramsay, T. Villaverde, R. Garilleti, J. G. Burleigh, Stuart F. McDaniel, M. Flagmeier, Jurgen Nieuwkoop, Arno van der Pluijm, Florian Hans, F. Lara, I. Draper","doi":"10.1111/jse.13040","DOIUrl":"https://doi.org/10.1111/jse.13040","url":null,"abstract":"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.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":" 59","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138961297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biogeographic analysis based on phylogenomic data supports multiple ancient dispersals that facilitated the eastern Asia–North America–Mexico disjunction in the subfamily Linnaeoideae (Caprifoliaceae)","authors":"Hong-Xin Wang, Diego F. Morales‐Briones, Jacob B. Landis, Jun Wen, Hua‐Feng Wang","doi":"10.1111/jse.13036","DOIUrl":"https://doi.org/10.1111/jse.13036","url":null,"abstract":"The small subfamily Linnaeoideae of Caprifoliaceae exhibits a disjunct distribution in Eurasia and North America, including Mexico, with most taxa occurring in eastern Asia or Mexico and the monospecific Linnaea Gronov. ex L. having a circumboreal to north temperate distribution. We sampled 17 of the 20 species representing all Linnaeoideae genera and used nuclear (target enrichment) and complete plastome sequence data to reconstruct the phylogeny. Our results show strong topological conflicts between nuclear and plastid data, especially concerning Dipelta Maxim. and Diabelia Landrein, supporting hybridization events complicating the deep diversification. Nuclear data were used for divergence time estimation and ancestral area reconstruction. The divergence time between the Mexican Vesalea M. Martens & Galeotti and the Linnaea clade was dated to 39.5 Ma, with a 95% highest posterior density of 28.2 Ma (mid‐Oligocene) to 45.2 Ma (mid‐Eocene). Reconstructed ancestral areas support a widespread common ancestor of Linnaea plus Vesalea in Mexico and at least another area (eastern Asia, North America, or Europe). The biogeographic analysis, including fossils, supports the ancestral range of Linnaeoideae to be widespread in central and western China + Europe + Mexico, or eastern and northern Asia + central and western China + Mexico, or central and western China + North America + Mexico. The North Atlantic and/or the Bering land bridges may be important in the widespread distribution across continents in the Northern Hemisphere. Our study highlights the importance of utilizing fossils in biogeographic inferences andusing data from different genomes while reconstructing deep and shallow phylogenies of organisms.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":" 19","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138994987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Approaching inselberg biodiversity conservation through plant growth and dispersal strategies","authors":"Luiz Bondi, Camila M. Patreze, Ricardo P. Louro, Laura Jane M. Santiago","doi":"10.1111/jse.13041","DOIUrl":"https://doi.org/10.1111/jse.13041","url":null,"abstract":"Climate change is promoting global declines in plant diversity, which are expected to be more critical in islands or island-like ecosystems due to environmental constraints and isolation. The species' vulnerability to climate change (VUL) depends on their ability to cope with changes or mitigate them. Therefore, we investigate the influence of growth and dispersal strategies of species from the Sugarloaf Rock Complex, Brazil, an island-like ecosystem, on their niche breadth (NB), long-dispersal (LD) capacity, and geographical range (GR). Besides, we evaluate the potential use of these strategies as indicators of species' VUL. We found that rock specialists exhibit narrower NB, lower LD capacity, and a more restricted GR when compared to other species. We also found that 63% of rock specialists are found in conservation red-lists and they are more vulnerable to climate change than woody plants. Conversely, self-dispersed plants are expected to be less vulnerable to climate change when compared to species with other dispersal mechanisms. Species vulnerable to climate change are 14 times more likely to be included in conservation red lists, and it might indicate that the species' VUL might also describe the species' vulnerability to other anthropogenic threats. Still, we suggest conservation attention on some species that are expected to be vulnerable to climate change but were not yet included in conservation red lists. We advocate for more efforts to ensure the conservation aspects of different functional groups in which inselbergs might not only offer isolation but also a refuge opportunity.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"47 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138691720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RAD-seq data provide new insights into biogeography, diversity anomaly, and species delimitation in eastern Asian–North American disjunct clade Benthamidia of Cornus (Cornaceae)","authors":"Zhi-Yuan Du,&nbsp;Jin Cheng,&nbsp;Qiu-Yun (Jenny) Xiang","doi":"10.1111/jse.13037","DOIUrl":"10.1111/jse.13037","url":null,"abstract":"<p>The big-bracted dogwood clade <i>Benthamidia</i> of <i>Cornus</i> is a typical example of the well-known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD-seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras. We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA. Finally, we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern. Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans-Beringian ancestral distribution of the clade <i>Benthamidia</i> in the mid-Oligocene, dispersal from Mexico to eastern United States in the mid-Miocene, and early diversification of the EA clade in SW China. Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade. Species delimitation analysis suggested 17 species in the clade <i>Benthamidia</i>, including all recognized subspecies. By integrating the results of molecular data with morphology, we proposed to retain the subspecies without changing their ranks. Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence.</p>","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":"62 1","pages":"1-19"},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jse.13037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138691820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}