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Zhang G, Yang J, Zhang C, Jiao B, Panero JL, Cai J, Zhang ZR, Gao LM, Gao T, Ma H. Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution. PLANT COMMUNICATIONS 2024; 5:100851. [PMID: 38409784 PMCID: PMC11211554 DOI: 10.1016/j.xplc.2024.100851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/22/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Convergent morphological evolution is widespread in flowering plants, and understanding this phenomenon relies on well-resolved phylogenies. Nuclear phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups, but it is limited to taxa with available fresh materials. Asteraceae, which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood, show multiple examples of convergent evolution. Nuclear Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes, but many phylogenetic and evolutionary questions regarding subtribes and genera remain, owing to limited sampling. Here, we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized subtribes. Ancestral character reconstruction supports multiple convergent evolutionary events in Asteraceae, with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups, respectively. Presence of the calyx-related pappus may have been especially important for the success of some subtribes and genera. Molecular evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology, including capitulum inflorescences and bilaterally symmetric flowers, potentially promoting the diversification of Asteraceae. Subsequent divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic flowers. This phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA; State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Caifei Zhang
- Wuhan Botanical Garden and Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bohan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - José L Panero
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Lijiang National Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan 674100, China.
| | - Tiangang Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, State College, PA 16801, USA.
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Liu J, An Z, Lin G. Intra-leaf heterogeneities of hydrogen isotope compositions in leaf water and leaf wax of monocots and dicots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:145258. [PMID: 33513516 DOI: 10.1016/j.scitotenv.2021.145258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/27/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Several recent studies showed that leaf wax n-alkane δ2H values (δ2Hwax) within a leaf were heterogeneous in a small number of species. It still remains unclear whether the heterogeneity of intra-leaf δ2Hwax values is general for various species, how δ2Hwax values vary spatially and temporally, and whether there is a common explanation for the intra-leaf δ2Hwax heterogeneity in higher plants. Here we compared the hydrogen isotope compositions of leaf wax and corresponding leaf water (δ2Hlw) across leaf sections among a variety of monocot and dicot plant species. There is significant and consistent heterogeneity for both δ2Hwax and δ2Hlw, i.e., base-to-tip 2H-enrichment for monocots (except Hemerocallis citrina, and Dactylis glomerata) whereas base-to-tip and center-to-edge increases in δ2Hwax and δ2Hlw for dicots. The consistent occurrence of variations of δ2Hlw and δ2Hwax values within a leaf imply that δ2Hwax values probably inherit point-to-pint from in-situ δ2Hlw values, and thus the intra-leaf δ2Hwax heterogeneity mainly results from the spatial pattern of intra-leaf δ2Hlw values associated with veinal structures between dicots and monocots. The general heterogeneity of intra-leaf δ2Hwax values further intensifies that it is necessarily needed for in-depth understanding leaf wax biomarker.
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Affiliation(s)
- Jinzhao Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, CAS, Xi'an 710061, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
| | - Zhisheng An
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, CAS, Xi'an 710061, China
| | - Guanghui Lin
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
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Liu H, Liu W. Hydrogen isotope fractionation variations of n-alkanes and fatty acids in algae and submerged plants from Tibetan Plateau lakes: Implications for palaeoclimatic reconstruction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133925. [PMID: 31756850 DOI: 10.1016/j.scitotenv.2019.133925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
The hydrogen isotope compositions (δD) of n-alkanes and fatty acids (FAs) are widely applied in palaeoclimatic reconstructions, and the determinations of their hydrogen isotope fractionation factor values (ε) are vital for quantitatively reconstructing past precipitation variations. Currently, studies on n-alkane and FA ε values focus on terrestrial plants, which, however, show large uncertainties because of the influence of evapotranspiration. Therefore, in this study, we analysed the ε values of algae and submerged plants immersed in lakes, which are not affected by evapotranspiration, to understand the hydrogen isotope fractionation of plant lipid synthesis. By investigating the δD values of lipids (n-alkanes and FAs) in algae and submerged plants and the δD values of co-existing water (including lake bottom water, surface sediment water, and leaf water of algae and submerged plants) from five Tibetan Plateau lakes, we find that the n-alkane ε values of algae and submerged plants show narrow changes, ranging from -176 to -159‰ and -167 to -142‰, respectively. The FA ε values of algae and submerged plants also show small variations, ranging from -160 to -121‰ (except Chara) and -161 to -138‰, respectively. Therefore, the average biosynthetic hydrogen isotope fractionation of these plants is -162‰ for n-alkanes and -145‰ for FAs, and the small ε differences between FAs and n-alkanes can be related to the different magnitudes of FA utilization in n-alkane synthesis. Finally, we find that the biosynthetic hydrogen isotope fractionation factors of aquatic plants are close to those of terrestrial grasses but slightly more negative than those of terrestrial woody plants. Thus, our results are helpful for understanding the hydrogen isotope fractionation variations in terrestrial plant lipids, which is beneficial for palaeohydrological reconstructions.
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Affiliation(s)
- Hu Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguo Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
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Liu J, An Z. Variations in hydrogen isotopic fractionation in higher plants and sediments across different latitudes: Implications for paleohydrological reconstruction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:470-478. [PMID: 30199691 DOI: 10.1016/j.scitotenv.2018.09.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Sedimentary δDn-alkane value is widely utilized as a reliable proxy for paleo-hydrological reconstruction. Applications of this proxy must be based upon a globally clear understanding of the relationship between leaf wax δDn-alkane values and precipitation δD (δDp), defined as apparent fractionation (εapp). However, there is a critical concern about whether relatively constant εapp values exist across different latitudes. In this study, we systematically analyzed the variations of available εapp with latitudes based upon two compiled-new databases of higher plants and sediments over the world. We found that the total average εapp was relatively constant, i.e., -116 ± 5‰ (n = 941), in higher plants across different latitudes without consideration of plant types (e.g., dicots, monocots, gymnosperms), and was still constant but slightly lower average εapp, i.e., -125 ± 6‰ (n = 460), in sediments across the latitudes. The slightly lower average εapp in sediments relative to higher plants probably derived from the contribution of aquatic plants with isotopically D-depleted εapp in lake sediments. Interestingly, with consideration of plant types, average εapp increased in dicots but decreased in monocots slightly from low to high latitudes. The counteraction of these competing trends generates relatively constant average εapp values in higher plants, and resultantly constant average εapp values occur in sediments at the global scale. It is important to elaborate relatively constant εapp values from higher plants and sediments across different latitudes when sedimentary δDn-alkane is utilized as a proxy for paleohydrological reconstruction.
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Affiliation(s)
- Jinzhao Liu
- State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Zhisheng An
- State key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China
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Liu J, An Z, Wang Z, Wu H. Using δD n-alkane as a proxy for paleo-environmental reconstruction: A good choice to sample at the site dominated by woods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:554-559. [PMID: 28494281 DOI: 10.1016/j.scitotenv.2017.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/14/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Some studies have demonstrated that leaf wax δDn-alkane values for a single species varied significantly with seasons. However, it is still not clear that the seasonality patterns of leaf wax δDn-alkane values in higher plants. Meanwhile, few efforts have been pursued to assess the effect of the light slopes (sunny vs. cloudy) on leaf wax δDn-alkane values. In this study, we systematically investigated plant wax δDn-alkane values and soil n-alkane δD values along different light slopes in different seasons (spring vs. autumn), as well as the relationship of n-alkane δD values between plant leaves and soil. We found that plant wax δDn-alkane values were D-enriched by ca. 20‰ in spring relative to autumn, and ca. 10‰ in the sunny slope than in the cloudy slope. Moreover, surface soil n-alkane δD values varied consistently with plant wax δDn-alkane values for different seasons and light slopes. More importantly, plant wax δDn-alkane values showed clear seasonal variations, but varied slightly with light slopes. The variations of plant wax δDn-alkane values can be recorded in soil n-alkane δDn-alkane values. In addition, we found that leaf wax δDn-alkane values in a majority of species differed significantly among woods, non-woods and grasses at a site. Therefore, we suggested a good choice to sample at the site dominated by woods when leaf wax δDn-alkane values are utilized as a proxy for the reconstruction of the paleoenvironment.
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Affiliation(s)
- Jinzhao Liu
- School of Human Settlements and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China; State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710075, China.
| | - Zhisheng An
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710075, China
| | - Zheng Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710075, China
| | - Huawu Wu
- Key Laboratory of Watershed Geographic Sciences, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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Liu J, Liu W, An Z, Yang H. Different hydrogen isotope fractionations during lipid formation in higher plants: Implications for paleohydrology reconstruction at a global scale. Sci Rep 2016; 6:19711. [PMID: 26806719 PMCID: PMC4726312 DOI: 10.1038/srep19711] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 12/16/2015] [Indexed: 12/01/2022] Open
Abstract
Leaf wax δDn-alkane values have shown to differ significantly among plant life forms (e.g., among grasses, shrubs, and trees) in higher plants. However, the underlying causes for the differences in leaf wax δDn-alkane values among different plant life forms remain poorly understood. In this study, we observed that leaf wax δDn-alkane values between major high plant lineages (eudicots versus monocots) differed significantly under the same environmental conditions. Such a difference primarily inherited from different hydrogen biosynthetic fractionations (εwax-lw). Based upon a reanalysis of the available leaf wax δDn-alkane dataset from modern plants in the Northern Hemisphere, we discovered that the apparent hydrogen fractionation factor (εwax-p) between leaf wax δDn-alkane values of major angiosperm lineages and precipitation δD values exhibited distinguishable distribution patterns at a global scale, with an average of -140‰ for monocotyledonous species, -107‰ for dicotyledonous species. Additionally, variations of leaf wax δDn-alkane values and the εwax-p values in gymnosperms are similar to those of dicotyledonous species. Therefore, the data let us believe that biological factors inherited from plant taxonomies have a significant effect on controlling leaf wax δDn-alkane values in higher plants.
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Affiliation(s)
- Jinzhao Liu
- School of Human Settlements and Civil Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- State Key Laboratory of Loess and Quaternary Geology, IEE, CAS, Xi’an 710075, China
| | - Weiguo Liu
- School of Human Settlements and Civil Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- State Key Laboratory of Loess and Quaternary Geology, IEE, CAS, Xi’an 710075, China
| | - Zhisheng An
- State Key Laboratory of Loess and Quaternary Geology, IEE, CAS, Xi’an 710075, China
| | - Hong Yang
- Laboratory for Terrestrial Environments, College of Arts and Sciences, Bryant University, Smithfield, RI 02917, USA
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