Both hybridization and intraspecific morphological variation across environmental gradients complicate species delineation. We aimed to discern both possibilities that may blur species boundaries in the Carpinus viminea–Carpinus laxiflora–Carpinus londoniana species complex. We conducted statistical analyses on 535 specimens encompassing the entire distribution of this species complex to identify phenotypic clusters. Additionally, we analyzed genetic divergence and probable hybridization between clusters using 76 individuals from 37 populations. Based on phenotypic and genetic clusters, we tentatively recognized four species: C. viminea, C. fargesii, C. laxiflora, and C. londoniana. Except for rare overlapping distributions between C. fargesii and C. londoniana, the redefined four species are mostly allopatric to each another based on their distributions. The morphological delimitation, species boundary and distribution of each species differ distinctly from past taxonomic treatments. For example, specimens previously identified under C. viminea, in fact, belong to three different species. Hybrids between C. fargesii and C. londoniana exhibit morphological traits similar to C. viminea, thereby contributing to difficulties in determining species boundaries and outlining species distributions. These findings suggest that local selection and geographical isolation may together have promoted both phenotypic and genetic divergences within this species complex. However, interspecific hybridization blurs species boundaries by producing hybrids with phenotypic similarity in addition to intraspecific variation. This study emphasizes the importance of statistical analyses of population-level morphological and genetic variations across major distributional ranges for an integrative delimitation of species boundaries and the identification of hybridization and hybrids.
跨越环境梯度的杂交和种内形态变异使物种划分变得复杂。我们的目标是辨别这两种可能，它们可能会模糊维米尼亚栎-腊叶栎-伦敦栎物种群的物种界限。我们对涵盖该物种群整个分布区的 535 个标本进行了统计分析，以确定表型集群。此外，我们还利用来自 37 个种群的 76 个个体分析了集群间的遗传差异和可能的杂交。根据表型和遗传聚类，我们初步确认了四个物种：C. viminea、C. fargesii、C. laxiflora 和 C. londoniana。除了 C. fargesii 和 C. londoniana 的分布有极少的重叠外，根据它们的分布情况，重新定义的四个物种大多是同域物种。每个物种的形态划界、物种边界和分布都与过去的分类方法有明显不同。例如，以前认定为 C. viminea 的标本实际上属于三个不同的种。C.fargesii和C.londoniana的杂交种表现出与C. viminea相似的形态特征，从而给确定物种界线和概述物种分布造成困难。这些发现表明，当地选择和地理隔离可能共同促进了该物种群的表型和遗传分化。然而，种间杂交除了产生种内变异外，还产生了表型相似的杂交种，从而模糊了物种界限。这项研究强调了对主要分布区种群水平的形态和遗传变异进行统计分析对于综合划定物种边界以及鉴定杂交和杂交种的重要性。
{"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}
Martha Kandziora, Juan M. Gorospe, Luciana Salomon, Diana L. A. Vásquez, Maria Pinilla Vargas, Filip Kolář, Petr Sklenář, Roswitha Schmickl
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.
{"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}
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
Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally, Eucalyptus was defined by its operculum, but when phylogenies placed Angophora, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. Yet, generic delimitation in the tribe Eucalypteae remains uncertain. Here, we address these problems using phylogenetic analysis with the largest molecular data set to date. We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multispecies coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among Arillastrum, Angophora, Eucalyptus, and Corymbia using Shimodaira's approximately unbiased test. Phylogenetic mapping was used to explore the evolution of perianth traits. Monophyly of Corymbia relative to Angophora was decisively rejected. All alternative relationships among the seven currently recognized Eucalypteae genera imply homoplasy in the evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades, except that the expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears to be a reversal to the plesiomorphic perianth structure. Here, we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations. We also define and name three sections within Blakella (Blakella sect. Blakella, Blakella sect. Naviculares, and Blakella sect. Maculatae), and two series within Blakella sect. Maculatae (Blakella ser. Maculatae and Blakella ser. Torellianae). Corymbia is reduced to the red bloodwoods.
{"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}
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
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.
{"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}
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.
{"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}
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
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.
目前，有多种基因组技术可供使用，而且价格相对低廉。然而，并不是所有的基因组技术都能在叶绿体系统学中得到同等的应用。在本研究中，我们应用下一代测序技术鉴定了无法通过形态分析或桑格测序方法归入一个分类群的样本。这些样本与一种形态神秘的苔藓相对应，该苔藓在过去二十年中遍布西欧。它们的配子体出现了一些异常，在极少数情况下，孢子体也会出现异常。最明显的变化与叶片的形状有关。从形态上看，所有标本都与莱温斯基亚属的苔藓一致，而变化最小的标本可能属于莱温斯基亚-阿菲尼斯复合体。我们首先尝试使用多达七种分子标记来鉴定标本，但结果并不令人满意。因此，我们使用 GoFlag 408 鞭毛虫陆生植物探针集进行靶向富集产生的数据来阐明它们的身份。我们的结果表明，所有谜样都对应于一个物种，即 L. affinis s.str.。这种方法提供了必要的分辨率，使我们能够有把握地鉴定这些具有挑战性的样本，并可能成为处理类似情况（尤其是叶绿体）的有力工具。
{"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}
Hong-Xin Wang, Diego F. Morales‐Briones, Jacob B. Landis, Jun Wen, Hua‐Feng Wang
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.
{"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}
Luiz Bondi, Camila M. Patreze, Ricardo P. Louro, Laura Jane M. Santiago
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.
{"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}
The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the well-known eastern Asia (EA) and North America (NA) floristic disjunction, with greater species diversity in EA than in NA. The lineage provides an opportunity to explore factors contributing to the plant diversity unevenness between EA and NA and test hypotheses on the origin of disjunct distribution from a phylogenetic perspective. We generated RAD-seq data, conducted phylogenomic and biogeographic analyses for the clade with sampling of all species (9) and subspecies (10) currently recognized in floras. We also assessed species delineation and calculated phylogenetic diversity to evaluate the diversity unevenness between EA and NA. Finally, we examined variation of diversification rates and ecological niches on the phylogeny to explore potential causes underlying the observed diversity pattern. Our results revealed phylogenetic relationships congruent with previous studies and suggested a trans-Beringian ancestral distribution of the clade Benthamidia in the mid-Oligocene, dispersal from Mexico to eastern United States in the mid-Miocene, and early diversification of the EA clade in SW China. Our results also confirmed greater phylogenetic diversity and diversification rate of the EA clade. Species delimitation analysis suggested 17 species in the clade Benthamidia, including all recognized subspecies. By integrating the results of molecular data with morphology, we proposed to retain the subspecies without changing their ranks. Our data suggested increased diversification rate in EA as an intrinsic factor explaining the greater species diversity in the region driven mainly by biogeographic isolation and partially by niche divergence.
山茱萸大苞片山茱萸支系（Benthamidia）是众所周知的亚洲东部（EA）和北美洲（NA）植物区系不一致的典型例子，EA的物种多样性高于NA。该品系为我们提供了一个机会，以探索造成东亚和北美植物多样性不均衡的因素，并从系统发育的角度检验关于植物不一致分布起源的假说。我们生成了 RAD-seq 数据，对该支系进行了系统发生组学和生物地理学分析，并对目前在植物学中公认的所有物种（9 个）和亚种（10 个）进行了取样。我们还评估了物种划分并计算了系统发育多样性，以评估 EA 和 NA 之间的多样性不均衡性。最后，我们研究了系统发育上的多样化率和生态位的变化，以探索观察到的多样性模式的潜在原因。我们的研究结果表明，EA支系的系统发生关系与之前的研究结果一致，并表明Benthamidia支系的祖先分布在更新世中期的跨白垩纪，在中新世中期从墨西哥扩散到美国东部，并在中国西南部早期分化。我们的研究结果还证实了EA支系具有更高的系统发育多样性和分化率。物种划分分析表明，Benthamidia 支系中有 17 个物种，包括所有公认的亚种。通过将分子数据结果与形态学结果相结合，我们建议保留这些亚种而不改变其等级。我们的数据表明，东亚地区物种多样性增加的内在因素主要是生物地理隔离，部分是生态位分化。
{"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, Jin Cheng, 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}
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