Andrés A. Del Risco, Diego A. Chacón, Lucia Ángel, David A. García
Since the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family-level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.
{"title":"Assembling an illustrated family-level tree of life for exploration in mobile devices","authors":"Andrés A. Del Risco, Diego A. Chacón, Lucia Ángel, David A. García","doi":"10.1111/jse.13053","DOIUrl":"https://doi.org/10.1111/jse.13053","url":null,"abstract":"Since the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family-level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139665575","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}
Heng-Ling Zhou, Lei Wang, Yun-Xia Yue, Zhi Luo, Shun-Jie Wang, Li-Guo Zhou, Li-Jun Luo, Hui Xia, Ming Yan
The soil-nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH4+) and dry fields (mainly in the form of nitrate, NO3−), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE-related traits among rice landraces as well as the genetic differentiation between NUE-associated genes and quantitative trait loci (QTLs). The japonica upland and lowland rice ecotypes showed large differences in their NUE-related traits such as the absorption ability for NH4+ and NO3−. The indica upland and lowland rice exhibited similar performances when cultivated in solutions containing NH4+ or NO3− or when planted in paddy or dry fields. However, the indica upland rice possessed a greater ability to absorb NO3−. We identified 76 QTLs for 25 measured traits using genome-wide association analysis. The highly differentiated NUE-associated genes or QTLs between ecotypes were rarely shared by japonica and indica subspecies, indicating an independent genetic basis for their soil-nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil-nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the japonica and indica subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil-nitrogen conditions and have implications for the improvement of NUE.
{"title":"Independent genetic differentiation between upland and lowland rice ecotypes within japonica and indica subspecies during their adaptations to different soil-nitrogen conditions","authors":"Heng-Ling Zhou, Lei Wang, Yun-Xia Yue, Zhi Luo, Shun-Jie Wang, Li-Guo Zhou, Li-Jun Luo, Hui Xia, Ming Yan","doi":"10.1111/jse.13046","DOIUrl":"https://doi.org/10.1111/jse.13046","url":null,"abstract":"The soil-nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH<sub>4</sub><sup>+</sup>) and dry fields (mainly in the form of nitrate, NO<sub>3</sub><sup>−</sup>), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE-related traits among rice landraces as well as the genetic differentiation between NUE-associated genes and quantitative trait loci (QTLs). The <i>japonica</i> upland and lowland rice ecotypes showed large differences in their NUE-related traits such as the absorption ability for NH<sub>4</sub><sup>+</sup> and NO<sub>3</sub><sup>−</sup>. The <i>indica</i> upland and lowland rice exhibited similar performances when cultivated in solutions containing NH<sub>4</sub><sup>+</sup> or NO<sub>3</sub><sup>−</sup> or when planted in paddy or dry fields. However, the <i>indica</i> upland rice possessed a greater ability to absorb NO<sub>3</sub><sup>−</sup>. We identified 76 QTLs for 25 measured traits using genome-wide association analysis. The highly differentiated NUE-associated genes or QTLs between ecotypes were rarely shared by <i>japonica</i> and <i>indica</i> subspecies, indicating an independent genetic basis for their soil-nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil-nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the <i>japonica</i> and <i>indica</i> subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil-nitrogen conditions and have implications for the improvement of NUE.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555732","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}
Darya Khan, AJ Harris, Qamar U. Zaman, Hong-Xin Wang, Jun Wen, Jacob B. Landis, Hua-Feng Wang
The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1438–1870 species within approximately 130 genera predominantly distributed from northern Canada to Patagonia. Four centers of diversity from Central and North America (Chihuahua, Puebla-Oaxaca, Sonora-Sinaloan, and Jalisco) and three centers of diversity from South America (Southern Central Andes, Caatinga, and Mara Atlantica) have played a pivotal role in disbursing cacti around the globe. Mexico is considered the richest area in cacti species with close to 563 species grouped into 50 genera. Approximately 118 species have been domesticated by Mesoamerican people as food crops and for ornamental purposes. Cacti inhabit a wide range of ecosystems and climate regions, ranging from tropical to subtropical and from arid to semiarid regions. Species belonging to the genus Opuntia are the major food crop producers in the family. Cacti have derived characteristics from familial synapomorphies within the Caryophyllales. Reproduction occurs through pollination facilitated by birds, bats, bees, and other insects. Climate variability, whether natural or human-induced threatens global crop production including high temperatures, salinity, drought, flood, changes in soil pH, and urbanization. Cacti have several adaptations that are important for coping with abiotic stresses, such as crassulacean acid metabolism (CAM photosynthesis), as well as modifications to root and stem physiological pathways. This review aims to provide a comprehensive view of the fruit crops in Cactaceae, including their evolution, worldwide distribution, and the environmental factors impacting cultivation.
{"title":"The evolutionary history and distribution of cactus germplasm resources, as well as potential domestication under a changing climate","authors":"Darya Khan, AJ Harris, Qamar U. Zaman, Hong-Xin Wang, Jun Wen, Jacob B. Landis, Hua-Feng Wang","doi":"10.1111/jse.13042","DOIUrl":"https://doi.org/10.1111/jse.13042","url":null,"abstract":"The angiosperm family Cactaceae, a member of the Caryophyllales, is a large and diverse group of stem succulents comprising 1438–1870 species within approximately 130 genera predominantly distributed from northern Canada to Patagonia. Four centers of diversity from Central and North America (Chihuahua, Puebla-Oaxaca, Sonora-Sinaloan, and Jalisco) and three centers of diversity from South America (Southern Central Andes, Caatinga, and Mara Atlantica) have played a pivotal role in disbursing cacti around the globe. Mexico is considered the richest area in cacti species with close to 563 species grouped into 50 genera. Approximately 118 species have been domesticated by Mesoamerican people as food crops and for ornamental purposes. Cacti inhabit a wide range of ecosystems and climate regions, ranging from tropical to subtropical and from arid to semiarid regions. Species belonging to the genus <i>Opuntia</i> are the major food crop producers in the family. Cacti have derived characteristics from familial synapomorphies within the Caryophyllales. Reproduction occurs through pollination facilitated by birds, bats, bees, and other insects. Climate variability, whether natural or human-induced threatens global crop production including high temperatures, salinity, drought, flood, changes in soil pH, and urbanization. Cacti have several adaptations that are important for coping with abiotic stresses, such as crassulacean acid metabolism (CAM photosynthesis), as well as modifications to root and stem physiological pathways. This review aims to provide a comprehensive view of the fruit crops in Cactaceae, including their evolution, worldwide distribution, and the environmental factors impacting cultivation.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555575","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}
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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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}
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