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Zhou P, Lei WS, Shi YK, Liu YZ, Luo Y, Li JH, Xiang XG. Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla. Int J Mol Sci 2024; 25:8500. [PMID: 39126069 PMCID: PMC11312641 DOI: 10.3390/ijms25158500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Wan-Shun Lei
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Ying-Kang Shi
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yi-Zhen Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666300, China;
| | - Ji-Hong Li
- Kadoorie Farm and Botanic Garden, Hong Kong Lam Kam Road, Tai Po, New Territories, Hong Kong 999077, China;
| | - Xiao-Guo Xiang
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
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Liu YY, Cao JL, Kan SL, Wang PH, Wang JL, Cao YN, Wang HW, Li JM. Phylogenomic analyses sheds new light on the phylogeny and diversification of Corydalis DC. in Himalaya-Hengduan Mountains and adjacent regions. Mol Phylogenet Evol 2024; 193:108023. [PMID: 38342159 DOI: 10.1016/j.ympev.2024.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
The Himalaya-Hengduan Mountains (HHM), a renowned biodiversity hotspot of the world, harbors the most extensive habitats for alpine plants with extraordinary high levels of endemism. Although the general evolution pattern has been elucidated, the underlying processes driving spectacular radiations in many species-rich groups remain elusive. Corydalis DC. is widely distributed throughout the Northern Hemisphere containing more than 500 species, with high diversity in HHM and adjacent regions. Using 95 plastid genes, 3,258,640 nuclear single nucleotide polymorphisms (SNPs) and eight single-copy nuclear genes (SCNs) generated from genome skimming data, we reconstructed a robust time-calibrated phylogeny of Corydalis comprising more than 100 species that represented all subgenera and most sections. Molecular dating indicated that all main clades of Corydalis began to diverge in the Eocene, with the majority of extant species in HHM emerged from a diversification burst after the middle Miocene. Global pattern of mean divergence times indicated that species distributed in HHM were considerably younger than those in other regions, particularly for the two most species-rich clades (V and VI) of Corydalis. The early divergence and the recent diversification of Corydalis were most likely promoted by the continuous orogenesis and climate change associated with the uplift of the Qinghai-Tibetan Plateau (QTP). Our study demonstrates the effectivity of phylogenomic analyses with genome skimming data on the phylogeny of species-rich taxa, and sheds lights on how the uplift of QTP has triggered the evolutionary radiations of large plant genera in HHM and adjacent regions.
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Affiliation(s)
- Yan-Yan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China.
| | - Jia-Liang Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Sheng-Long Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China; Marine College, Shandong University, Weihai 264209, China
| | - Peng-Hang Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Jun-Li Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Ya-Nan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong-Wei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Jia-Mei Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China.
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Tayebi Z, Moghaddam M, Mahmoodi M, Kazempour-Osaloo S. Evolutionary history of an Irano-Turanian cushion-forming legume (Onobrychis cornuta). BMC PLANT BIOLOGY 2024; 24:204. [PMID: 38509474 PMCID: PMC10953250 DOI: 10.1186/s12870-024-04895-y] [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: 10/21/2023] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
The Irano-Turanian region is one of the largest floristic regions in the world and harbors a high percentage of endemics, including cushion-like and dwarf-shrubby taxa. Onobrychis cornuta is an important cushion-forming element of the subalpine/alpine flora of the Irano-Turanian floristic region. To specify the genetic diversity among the populations of this species (including individuals of O. elymaitica), we employed nrDNA ITS and two noncoding regions of plastid DNA (rpl32-trnL(UAG) and trnT(UGU)-trnL(UAA)). The most striking feature of O. cornuta assemblages was the unexpectedly high nucleotide diversity in both the nDNA and cpDNA dataset. In the analyses of nuclear and plastid regions, 25 ribotypes and 42 haplotypes were found among 77 and 59 accessions, respectively, from Iran, Turkey, and Afghanistan. Network analysis of the datasets demonstrated geographic differentiation within the species. Phylogenetic analyses of all dataset retrieved O. cornuta as a non-monophyletic species due to the inclusion of O. elymaitica, comprising four distinct lineages. In addition, our analyses showed cytonuclear discordance between both nuclear and plastid topologies regarding the position of some O. cornuta individuals. The underlying causes of this inconsistency remain unclear. However, we speculate that chloroplast capture, incomplete lineage sorting, and introgression were the main reasons for this event. Furthermore, molecular dating analysis indicated that O. cornuta originated in the early Pliocene (around 4.8 Mya) and started to diversify throughout the Pliocene and in particular the Pleistocene. Moreover, O. elymaitica was reduced to a subspecific rank within the species.
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Affiliation(s)
- Zahra Tayebi
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran, 14115-154
| | - Mahtab Moghaddam
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran, 14115-154
| | - Mohammad Mahmoodi
- Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 13185-116, Tehran, Iran
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran, 14115-154.
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Folk RA, Charboneau JLM, Belitz M, Singh T, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Siniscalchi CM. Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16299. [PMID: 38419145 DOI: 10.1002/ajb2.16299] [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: 08/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
PREMISE Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. METHODS Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents. RESULTS Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway. CONCLUSIONS Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Michael Belitz
- Florida Museum, University of Florida, Gainesville, FL, USA
| | - Tajinder Singh
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | | | - Douglas E Soltis
- Florida Museum, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Robert P Guralnick
- Florida Museum, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
- General Libraries, Mississippi State University, Mississippi State, MS, USA
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Xiao TW, Song F, Vu DQ, Feng Y, Ge XJ. The evolution of ephemeral flora in Xinjiang, China: insights from plastid phylogenomic analyses of Brassicaceae. BMC PLANT BIOLOGY 2024; 24:111. [PMID: 38360561 PMCID: PMC10868009 DOI: 10.1186/s12870-024-04796-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND The ephemeral flora of northern Xinjiang, China, plays an important role in the desert ecosystems. However, the evolutionary history of this flora remains unclear. To gain new insights into its origin and evolutionary dynamics, we comprehensively sampled ephemeral plants of Brassicaceae, one of the essential plant groups of the ephemeral flora. RESULTS We reconstructed a phylogenetic tree using plastid genomes and estimated their divergence times. Our results indicate that ephemeral species began to colonize the arid areas in north Xinjiang during the Early Miocene and there was a greater dispersal of ephemeral species from the surrounding areas into the ephemeral community of north Xinjiang during the Middle and Late Miocene, in contrast to the Early Miocene or Pliocene periods. CONCLUSIONS Our findings, together with previous studies, suggest that the ephemeral flora originated in the Early Miocene, and species assembly became rapid from the Middle Miocene onwards, possibly attributable to global climate changes and regional geological events.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Duc Quy Vu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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Moghaddam M, Wojciechowski MF, Kazempour-Osaloo S. Characterization and comparative analysis of the complete plastid genomes of four Astragalus species. PLoS One 2023; 18:e0286083. [PMID: 37220139 DOI: 10.1371/journal.pone.0286083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023] Open
Abstract
Astragalus is the largest flowering plant genus. We assembled the plastid genomes of four Astragalus species (Astragalus iranicus, A. macropelmatus, A. mesoleios, A. odoratus) using next-generation sequencing and analyzed their plastomes including genome organization, codon usage, nucleotide diversity, prediction of RNA editing and etc. The total length of the newly sequenced Astragalus plastomes ranged from 121,050 bp to 123,622 bp, with 110 genes comprising 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Comparative analysis of the chloroplast genomes of Astragalus revealed several hypervariable regions comprising three non-coding sites (trnQ(UUG)-accD, rps7 -trnV(GAC) and trnR(ACG)-trnN(GUU)) and four protein-coding genes (ycf1, ycf2, accD and clpP), which have potential as molecular markers. Positive selection signatures were found in five genes in Astragalus species including rps11, rps15, accD, clpP and ycf1. The newly sequenced species, A. macropelmatus, has an approximately 13-kb inversion in IR region. Phylogenetic analysis based on 75 protein-coding gene sequences confirmed that Astragalus form a monophyletic clade within the tribe Galegeae and Oxytropis is sister group to the Coluteoid clade. The results of this study may helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Astragalus and IRLC levels and investigating the phylogenetic relationships. Moreover, the newly plastid genomes sequenced have been increased the plastome data resources on Astragalus that can be useful in further phylogenomic studies.
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Affiliation(s)
- Mahtab Moghaddam
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Martin F Wojciechowski
- School of Life Science, Arizona State University, Tempe, Arizona, United States of America
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Helmstetter AJ, Zenil-Ferguson R, Sauquet H, Otto SP, Méndez M, Vallejo-Marin M, Schönenberger J, Burgarella C, Anderson B, de Boer H, Glémin S, Käfer J. Trait-dependent diversification in angiosperms: Patterns, models and data. Ecol Lett 2023; 26:640-657. [PMID: 36829296 DOI: 10.1111/ele.14170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 02/26/2023]
Abstract
Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties - trees that were larger, older or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics.
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Affiliation(s)
- Andrew J Helmstetter
- Fondation pour la recherche sur la biodiversité-CEntre de Synthèse et d'Analyse sur la Biodiversité, Montpellier, France
| | | | - Hervé Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marcos Méndez
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Bruce Anderson
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Sylvain Glémin
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- CNRS, Ecosystèmes Biodiversité Evolution (Université de Rennes), Rennes, France
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
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Bagheri A, Maassoumi AA, Brassac J, Blattner FR. Dated Phylogeny of Astragalus Section Stereothrix (Fabaceae) and Allied Taxa in the Hypoglottis Clade. BIOLOGY 2023; 12:biology12010138. [PMID: 36671830 PMCID: PMC9855906 DOI: 10.3390/biology12010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023]
Abstract
The Astragalus subgenus Hypoglottis Bunge, which consists of several sections, is one of the taxonomically most complicated groups in the genus. The Astragalus section Stereothrix Bunge belongs to this subgenus and is a significant element of the Irano-Turanian floristic region. A molecular phylogenetic analysis of this section and its closely related taxa using nuclear ribosomal DNA internal transcribed spacers (ITS) and external transcribed spacer (ETS) regions as well as plastid matK sequences were conducted. Parsimony analyses and Bayesian phylogenetic inference revealed that the section is not monophyletic in its current form, as some taxa belonging to closely related sections such as Hypoglottidei DC. and the Malacothrix Bunge group within the sect. Stereothrix render it paraphyletic. Moreover, species groups belonging to sect. Stereothrix are placed in different clades within the phylogenetic tree of subgenus Hypoglottis, which indicates polyphyly, i.e., multiple independent origins of taxa placed in the sect. Stereothrix. Molecular dating of the group estimated an age of 3.62 (1.73-5.62) My for this assemblage with the major diversification events happening during the last 2 My. Many species groups separated only within the last 0.5 to 1 My. Based on morphological and molecular data, we discuss the phylogenetic relationships of the groups and synonymy of species. In addition, the included taxa of sect. Hypoglottidei are not monophyletic and include species belonging to sects. Hololeuce, Koelziana, Malacothrix, Onobrychoideae, and Ornithodpodium group within the sect. Stereothrix taxa. We conclude that only an analysis including all groups and nearly all species of the sections within the Hypoglottis clade can finally result in an new evolutionary-based system for these taxa.
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Affiliation(s)
- Ali Bagheri
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Hezarjarib Street, Isfahan P.O. Box 81746-73441, Iran
- Correspondence: (A.B.); (F.R.B.)
| | - Ali Asghar Maassoumi
- Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran P.O. Box 13185-116, Iran
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
- Institute of Agricultural and Nutritional Sciences, Martin Luther University, D-06120 Halle, Germany
- Julius Kühn Institute (JKI), D-06484 Quedlinburg, Germany
| | - Frank R. Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany
- Correspondence: (A.B.); (F.R.B.)
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Feng J, Xiong Y, Su X, Liu T, Xiong Y, Zhao J, Lei X, Yan L, Gou W, Ma X. Analysis of Complete Chloroplast Genome: Structure, Phylogenetic Relationships of Galega orientalis and Evolutionary Inference of Galegeae. Genes (Basel) 2023; 14:176. [PMID: 36672917 PMCID: PMC9859028 DOI: 10.3390/genes14010176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/24/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Galega orientalis, a leguminous herb in the Fabaceae family, is an ecologically and economically important species widely cultivated for its strong stress resistance and high protein content. However, genomic information of Galega orientalis has not been reported, which limiting its evolutionary analysis. The small genome size makes chloroplast relatively easy to obtain genomic sequence for phylogenetic studies and molecular marker development. Here, the chloroplast genome of Galega orientalis was sequenced and annotated. The results showed that the chloroplast genome of G. orientalis is 125,280 bp in length with GC content of 34.11%. A total of 107 genes were identified, including 74 protein-coding genes, 29 tRNAs and four rRNAs. One inverted repeat (IR) region was lost in the chloroplast genome of G. orientalis. In addition, five genes (rpl22, ycf2, rps16, trnE-UUC and pbf1) were lost compared with the chloroplast genome of its related species G. officinalis. A total of 84 long repeats and 68 simple sequence repeats were detected, which could be used as potential markers in the genetic studies of G. orientalis and related species. We found that the Ka/Ks values of three genes petL, rpl20, and ycf4 were higher than one in the pairwise comparation of G. officinalis and other three Galegeae species (Calophaca sinica, Caragana jubata, Caragana korshinskii), which indicated those three genes were under positive selection. A comparative genomic analysis of 15 Galegeae species showed that most conserved non-coding sequence regions and two genic regions (ycf1 and clpP) were highly divergent, which could be used as DNA barcodes for rapid and accurate species identification. Phylogenetic trees constructed based on the ycf1 and clpP genes confirmed the evolutionary relationships among Galegeae species. In addition, among the 15 Galegeae species analyzed, Galega orientalis had a unique 30-bp intron in the ycf1 gene and Tibetia liangshanensis lacked two introns in the clpP gene, which is contrary to existing conclusion that only Glycyrrhiza species in the IR lacking clade (IRLC) lack two introns. In conclusion, for the first time, the complete chloroplast genome of G. orientalis was determined and annotated, which could provide insights into the unsolved evolutionary relationships within the genus Galegeae.
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Affiliation(s)
- Junjie Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Science, Chengdu 611130, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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11
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Phylogeny and Historical Biogeography of Veronica Subgenus Pentasepalae (Plantaginaceae): Evidence for Its Origin and Subsequent Dispersal. BIOLOGY 2022; 11:biology11050639. [PMID: 35625367 PMCID: PMC9138021 DOI: 10.3390/biology11050639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 11/19/2022]
Abstract
Simple Summary The Irano-Turanian phytogeographical region is considered a biodiversity reservoir for adjacent regions. The present phylogeographic study suggests that Veronica subgenus Pentasepalae originated in the Iranian plateau and was dispersed via a North African route to the Mediterranean and the Euro-Siberian regions. These findings highlight the importance of the Iranian plateau as a center of origin for many temperate plant species. Our results also resolve several taxonomic and phylogenetic issues surrounding the Southwest Asian species of this subgenus. Abstract Veronica subgenus Pentasepalae is the largest subgenus of Veronica in the Northern Hemisphere with approximately 80 species mainly from Southwest Asia. In order to reconstruct the phylogenetic relationships among the members of V. subgenus Pentasepalae and to test the “out of the Iranian plateau” hypothesis, we applied thorough taxonomic sampling, employing nuclear DNA (ITS) sequence data complimented with morphological studies and chromosome number counts. Several high or moderately supported clades are reconstructed, but the backbone of the phylogenetic tree is generally unresolved, and many Southwest Asian species are scattered along a large polytomy. It is proposed that rapid diversification of the Irano-Turanian species in allopatric glacial refugia and a relatively high rate of extinction during interglacial periods resulted in such phylogenetic topology. The highly variable Asian V. orientalis–V. multifida complex formed a highly polyphyletic assemblage, emphasizing the idea of cryptic speciation within this group. The phylogenetic results allow the re-assignment of two species into this subgenus. In addition, V. bombycina subsp. bolkardaghensis, V. macrostachya subsp. schizostegia and V. fuhsii var. linearis are raised to species rank and the new name V. parsana is proposed for the latter. Molecular dating and ancestral area reconstructions indicate a divergence age of about 9 million years ago and a place of origin on the Iranian Plateau. Migration to the Western Mediterranean region has likely taken place through a North African route during early quaternary glacial times. This study supports the assumption of the Irano-Turanian region as a source of taxa for neighboring regions, particularly in the alpine flora.
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12
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Chen YP, Turdimatovich TO, Nuraliev MS, Lazarević P, Drew BT, Xiang CL. Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae). Cladistics 2022; 38:429-451. [PMID: 35358338 DOI: 10.1111/cla.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/28/2022] Open
Abstract
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Maxim S Nuraliev
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Predrag Lazarević
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, 68849, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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13
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Genome Size and Chromosome Number Evaluation of Astragalus L. sect. Hymenostegis Bunge (Fabaceae). PLANTS 2022; 11:plants11030435. [PMID: 35161416 PMCID: PMC8838222 DOI: 10.3390/plants11030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022]
Abstract
Astragalus section Hymenostegis is one of the important characteristic elements of thorn-cushion formations in the Irano-Turanian floristic region. In this paper, we examined the chromosome number of 17 species (15 new reports) and provide estimates of genome size for 62 individuals belonging to 38 taxa of A. sect. Hymenostegis, some species outside this section, plus two Oxytropis species. Based on chromosome counts 11 species were found to be diploid (2n = 16), four species tetraploid (2n = 32) and two taxa hexaploid (2n = 48). From genome size measurements on silica-gel dried material, three ploidy levels (2x, 4x and 6x) were inferred, with a majority of species being diploid. The 2C values reach from 2.07 pg in diploid Astragalus zohrabi to 7.16 pg in hexaploid A. rubrostriatus. We found indications that species might occur with different cytotypes. A phylogenetic framework using nrDNA ITS sequences was constructed to understand the evolution of ploidy changes and genome sizes. It showed that genome size values among the studied taxa differ only slightly within ploidy levels and are nearly constant within most species and groups of closely related taxa within the genus Astragalus. The results of this study show that there is a rather strong correlation between genome sizes and chromosome numbers in sect. Hymenostegis. The resolution of the ITS-based phylogenetic tree is too low to infer evolutionary or environmental correlations of genome size differences. Polyploidization seems to contribute to the high species number in Astragalus, however, in sect. Hymenostegis it is not the main driver of speciation.
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14
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Li Z, Lathe RS, Li J, He H, Bhalerao RP. Towards understanding the biological foundations of perenniality. TRENDS IN PLANT SCIENCE 2022; 27:56-68. [PMID: 34561180 DOI: 10.1016/j.tplants.2021.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials' physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.
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Affiliation(s)
- Zheng Li
- State Key Laboratory for Conservation and Utilisation of Bio-Resources in Yunnan, Research Centre for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, 650091 Kunming, China.
| | - Rahul S Lathe
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
| | - Jinping Li
- State Key Laboratory for Conservation and Utilisation of Bio-Resources in Yunnan, Research Centre for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, 650091 Kunming, China
| | - Hong He
- State Key Laboratory for Conservation and Utilisation of Bio-Resources in Yunnan, Research Centre for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, 650091 Kunming, China
| | - Rishikesh P Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden.
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15
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Xia XM, Yang MQ, Li CL, Huang SX, Jin WT, Shen TT, Wang F, Li XH, Yoichi W, Zhang LH, Zheng YR, Wang XQ. Spatiotemporal evolution of the global species diversity of Rhododendron. Mol Biol Evol 2021; 39:6413646. [PMID: 34718707 PMCID: PMC8760938 DOI: 10.1093/molbev/msab314] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3,437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multispecies subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southward from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, that is, elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
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Affiliation(s)
- Xiao-Mei Xia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao-Qin Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cong-Li Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Xin Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fei Wang
- West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Sichuan 611834, China
| | - Xiao-Hua Li
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi 332900, China
| | - Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, Chiba 271-8510, Japan
| | - Le-Hua Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi 332900, China
| | - Yuan-Run Zheng
- West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Sichuan 611834, China.,State Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Charboneau JLM, Cronn RC, Liston A, Wojciechowski MF, Sanderson MJ. Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae). Genome Biol Evol 2021; 13:evab215. [PMID: 34534296 PMCID: PMC8486006 DOI: 10.1093/gbe/evab215] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation.
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Affiliation(s)
- Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Richard C Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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17
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Dorchin A, Shafir A, Neumann FH, Langgut D, Vereecken NJ, Mayrose I. Bee flowers drive macroevolutionary diversification in long-horned bees. Proc Biol Sci 2021; 288:20210533. [PMID: 34547912 PMCID: PMC8515878 DOI: 10.1098/rspb.2021.0533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The role of plant–pollinator interactions in the rapid radiation of the angiosperms have long fascinated evolutionary biologists. Studies have brought evidence for pollinator-driven diversification of various plant lineages, particularly plants with specialized flowers and concealed rewards. By contrast, little is known about how this crucial interaction has shaped macroevolutionary patterns of floral visitors. In particular, there is currently no empirical evidence that floral host association has increased diversification in bees, the most prominent group of floral visitors that essentially rely on angiosperm pollen. In this study, we examine how floral host preference influenced diversification in eucerine bees (Apidae, Eucerini), which exhibit large variations in their floral associations. We combine quantitative pollen analyses with a recently proposed phylogenetic hypothesis, and use a state speciation and extinction probabilistic approach. Using this framework, we provide the first evidence that multiple evolutionary transitions from host plants with accessible pollen to restricted pollen from ‘bee-flowers’ have significantly increased the diversification of a bee clade. We suggest that exploiting host plants with restricted pollen has allowed the exploitation of a new ecological niche for eucerine bees and contributed both to their colonization of vast regions of the world and their rapid diversification.
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Affiliation(s)
- Achik Dorchin
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, The Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Frank H Neumann
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein 2050, Johannesburg, South Africa
| | - Dafna Langgut
- Department of Archaeology and Ancient Near Eastern Cultures, and The Steinhardt Museum of Natural History, Tel Aviv University, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, The Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
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18
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Li J, Zhang Y, Ruhsam M, Milne RI, Wang Y, Wu D, Jia S, Tao T, Mao K. Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora. Cladistics 2021; 38:187-203. [PMID: 34551153 DOI: 10.1111/cla.12491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/15/2021] [Accepted: 08/27/2021] [Indexed: 12/16/2022] Open
Abstract
The Eastern Asia (EA) - North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii-Thuja sutchuenensis and a "disjunct clade", where western NA species T. plicata is sister to an EA-eastern NA disjunct Thuja occidentalis-Thuja koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, approximately 20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.
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Affiliation(s)
- Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Yujiao Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Richard Ian Milne
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3JH, UK
| | - Yi Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Dayu Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Shiyu Jia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Tongzhou Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, 610065, China.,College of Science, Tibet University, Lhasa, Xizang Autonomous Region, 850012, China
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19
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Krupitsky AV, Shapoval NA, Schepetov DM, Ekimova IA, Lukhtanov VA. Phylogeny, species delimitation and biogeography of the endemic Palaearctic tribe Tomarini (Lepidoptera: Lycaenidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The tribe Tomarini is represented by the sole genus Tomares, comprising about eight species distributed from the western Mediterranean to Central Asia. We carried out a multilocus phylogenetic and a biogeographical analysis to test the taxonomy of the genus by several molecular species delimitation methods and reveal patterns shaping the current distribution of Tomares. The phylogenetic analysis based on four molecular markers recovered the monophyly of the genus and recovered two deep-branching lineages: an African clade and an Asian clade. Species delimitation analyses suggested six or ten putative species depending on the method applied. The haplotype network analysis of the Tomares nogelii clade revealed no phylogeographical and taxonomic structure. We consider the taxon Tomares nesimachus (syn. nov.) a synonym of T. nogelii and reinstate Tomares callimachus dentata stat. rev. for populations from south-eastern Turkey. Tomares originated between the early Oligocene and the early Miocene, most probably in south-west Asia. The split of the most recent common ancestor of Tomares occurred between the middle-late Miocene and middle-late Pliocene, probably as a response to increasing aridification and habitat fragmentation. Differentiation of the Asian clade took place in south-west Asia during the Pliocene and Pleistocene and coincided temporally with the evolution of Tomares host plants of the genus Astragalus (Fabaceae).
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Affiliation(s)
- Anatoly V Krupitsky
- Department of Entomology, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, GSP-1, korp. 12, Moscow, Russia
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect 33, Moscow, Russia
| | - Nazar A Shapoval
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg, Russia
| | - Dmitry M Schepetov
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, GSP-1, korp. 12, Moscow, Russia
| | - Irina A Ekimova
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, GSP-1, korp. 12, Moscow, Russia
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg, Russia
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20
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Tian C, Li X, Wu Z, Li Z, Hou X, Li FY. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae). Front Genet 2021; 12:705482. [PMID: 34422006 PMCID: PMC8378255 DOI: 10.3389/fgene.2021.705482] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.
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Affiliation(s)
- Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiansong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Xiangyang Hou
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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21
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Duan L, Li SJ, Su C, Sirichamorn Y, Han LN, Ye W, Lôc PK, Wen J, Compton JA, Schrire B, Nie ZL, Chen HF. Phylogenomic framework of the IRLC legumes (Leguminosae subfamily Papilionoideae) and intercontinental biogeography of tribe Wisterieae. Mol Phylogenet Evol 2021; 163:107235. [PMID: 34146677 DOI: 10.1016/j.ympev.2021.107235] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
The inverted repeat-lacking clade (IRLC) is one of the most derived clades within the subfamily Papilionoideae of the legume family, and includes various economically important plants, e.g., chickpeas, peas, liquorice, and the largest genus of angiosperms, Astragalus. Tribe Wisterieae is one of the earliest diverged groups of the IRLC, and its generic delimitation and spatiotemporal diversification needs further clarifications. Based on genome skimming data, we herein reconstruct the phylogenomic framework of the IRLC, and infer the inter-generic relationships and historical biogeography of Wisterieae. We redefine tribe Caraganeae to contain Caragana only, and tribe Astragaleae is reduced to the Erophaca-Astragalean clade. The chloroplast capture scenario was hypothesized as the most plausible explanation of the topological incongruences between the chloroplast CDSs and nuclear ribosomal DNA trees in both the Glycyrrhizinae-Adinobotrys-Wisterieae clade and the Chesneyeae-Caraganeae-Hedysareae clade. A new name, Caragana lidou L. Duan & Z.Y. Chang, is proposed within Caraganeae. Thirteen genera are herein supported within Wisterieae, including a new genus, Villosocallerya L. Duan, J. Compton & Schrire, segregated from Callerya. Our biogeographic analyses suggest that Wisterieae originated in the late Eocene and its most recent common ancestor (MRCA) was distributed in continental southeastern Asia. Lineages of Wisterieae remained in the ancestral area from the early Oligocene to the early Miocene. By the middle Miocene, Whitfordiodendron and the MRCA of Callerya-Kanburia-Villosocallerya Clade became disjunct between the Sunda area and continental southeastern Asia, respectively; the MRCA of Wisteria migrated to North America via the Bering land bridge. The ancestor of Austrocallerya and Padbruggea migrated to the Wallacea-Oceania area, which split in the early Pliocene. In the Pleistocene, Wisteria brachybotrys, W. floribunda and Wisteriopsis japonica reached Japan, and Callerya cinerea dispersed to South Asia. This study provides a solid phylogenomic for further evolutionary/biogeographic/systematic investigations on the ecologically diverse and economically important IRLC legumes.
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Affiliation(s)
- Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shi-Jin Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Yotsawate Sirichamorn
- Silpakorn University, Department of Biology, Faculty of Science, Sanam Chandra Palace Campus, Nakhon Pathom 73000, Thailand
| | - Li-Na Han
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Wen Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Phan Ke Lôc
- Department of Botany and HNU, Faculty of Biology, VNU Hanoi University of Science (HUS), Hanoi, Viet Nam
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, D.C. 20013-7012, USA.
| | | | - Brian Schrire
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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22
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Su C, Duan L, Liu P, Liu J, Chang Z, Wen J. Chloroplast phylogenomics and character evolution of eastern Asian Astragalus (Leguminosae): Tackling the phylogenetic structure of the largest genus of flowering plants in Asia. Mol Phylogenet Evol 2020; 156:107025. [PMID: 33271371 DOI: 10.1016/j.ympev.2020.107025] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/01/2023]
Abstract
Astragalus, as the largest genus of the flowering plants, is well-known for its high species richness and morphological diversity. Previous studies suggested that many of the subgenera of Astragalus are not monophyletic and the phylogenetic relationships within the genus are still poorly known. In this study, we sampled 117 accessions of Astragalus and its close relatives, covering 55 sections of the genus plus 30 outgroup taxa to recover the main clades of eastern Asian Astragalus based on sequences of the whole chloroplast genome and 65 chloroplast CDSs. Astragalus is supported to be monophyletic and it is sister to the Oxytropis + Coluteoid clade. Within Astragalus, we recovered ten clades, and the ten clades differ substantially from Bunge's subgenera. The former segregate genus Astracantha is also monophyletic, but embedded within Astragalus s. str., supporting the merge of the spiny former genus Astracantha with Astragalus. We detected the atpF intron losses in the chloroplast genome of the Oxytropis + Coluteoid clade, i.e., the sister clade to Astragalus. Furthermore, we estimated the ancestral states of the trichome morphology and habit via the Bayesian Binary Method. The medifixed hair type is inferred to have developed at least five times and the annual habit originated at least six times. In addition, Astragalus is estimated to have originated in the mid Miocene (stem age, 16.09 Ma, 95% HPD: 12.46-20.50 Ma). The divergence times of the medifixed hair groups ranged from 4.03 to 0.87 Ma, mostly 2-1 Ma, which are correlated with the estimated phased uplifts of the Qinghai-Tibetan Plateau (QTP). We hypothesize that the uplifts of the QTP, which contributed to aridification in eastern Asia and the adjacent regions, may have accelerated the rapid speciation of Astragalus, especially the xerophilous groups (i.e. the medifixed hair groups).
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Affiliation(s)
- Chun Su
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China; Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA
| | - Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Peiliang Liu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jing Liu
- College of Life Sciences, Sichuan Agricultural University, Sichuan, China
| | - Zhaoyang Chang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA.
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23
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Barbolini N, Woutersen A, Dupont-Nivet G, Silvestro D, Tardif D, Coster PMC, Meijer N, Chang C, Zhang HX, Licht A, Rydin C, Koutsodendris A, Han F, Rohrmann A, Liu XJ, Zhang Y, Donnadieu Y, Fluteau F, Ladant JB, Le Hir G, Hoorn C. Cenozoic evolution of the steppe-desert biome in Central Asia. SCIENCE ADVANCES 2020; 6:eabb8227. [PMID: 33036969 PMCID: PMC7546705 DOI: 10.1126/sciadv.abb8227] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/20/2020] [Indexed: 05/26/2023]
Abstract
The origins and development of the arid and highly seasonal steppe-desert biome in Central Asia, the largest of its kind in the world, remain largely unconstrained by existing records. It is unclear how Cenozoic climatic, geological, and biological forces, acting at diverse spatial and temporal scales, shaped Central Asian ecosystems through time. Our synthesis shows that the Central Asian steppe-desert has existed since at least Eocene times but experienced no less than two regime shifts, one at the Eocene-Oligocene Transition and one in the mid-Miocene. These shifts separated three successive "stable states," each characterized by unique floral and faunal structures. Past responses to disturbance in the Asian steppe-desert imply that modern ecosystems are unlikely to recover their present structures and diversity if forced into a new regime. This is of concern for Asian steppes today, which are being modified for human use and lost to desertification at unprecedented rates.
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Affiliation(s)
- N Barbolini
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, Netherlands.
- Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - A Woutersen
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, Netherlands.
| | - G Dupont-Nivet
- Universität Potsdam, Institute of Geosciences, 14476 Potsdam, Germany
- Université de Rennes, CNRS, Géosciences Rennes-UMR 6118, F-35000 Rennes, France
- Key Laboratory of Orogenic Belts and Crustal Evolution, Peking University, Beijing 100871, China
| | - D Silvestro
- Department of Biology, University of Fribourg, Ch. De Musée 10, Fribourg, Switzerland
| | - D Tardif
- Institut de Physique du Globe, Paris 75005, France
| | - P M C Coster
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - N Meijer
- Universität Potsdam, Institute of Geosciences, 14476 Potsdam, Germany
| | - C Chang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - H-X Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - A Licht
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
| | - C Rydin
- Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden
- The Bergius Foundation, The Royal Swedish Academy of Sciences, Box 50005, SE-104 05 Stockholm, Sweden
| | - A Koutsodendris
- Institute of Earth Sciences, Heidelberg University, Heidelberg 69120, Germany
| | - F Han
- School of Earth Sciences, East China University of Technology, Nanchang 330013, Jiangxi, China
| | - A Rohrmann
- Universität Potsdam, Institute of Geosciences, 14476 Potsdam, Germany
| | - X-J Liu
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
| | - Y Zhang
- The First Monitoring and Application Center, China Earthquake Administration, Tianjin 300180, China
| | - Y Donnadieu
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE)/Institute Pierre Simon Laplace (IPSL), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA)-CNRS-Université de Versailles Saint Quentin-en-Yvelines (UVSQ), Université Paris-Saclay, Gif-sur-Yvette, France
- Aix-Marseille Université, CNRS, Institut pour la Recherche et le Développement (IRD), Collège de France, Centre de Recherche et d'Enseignement de Géosciences de l'Environnement (CEREGE), Aix-en-Provence, France
| | - F Fluteau
- Institut de Physique du Globe, Paris 75005, France
| | - J-B Ladant
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - G Le Hir
- Institut de Physique du Globe, Paris 75005, France
| | - C Hoorn
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, Netherlands.
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24
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Duan L, Harris A, Su C, Zhang ZR, Arslan E, Ertuğrul K, Loc PK, Hayashi H, Wen J, Chen HF. Chloroplast Phylogenomics Reveals the Intercontinental Biogeographic History of the Liquorice Genus (Leguminosae: Glycyrrhiza). FRONTIERS IN PLANT SCIENCE 2020; 11:793. [PMID: 32636856 PMCID: PMC7318913 DOI: 10.3389/fpls.2020.00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/18/2020] [Indexed: 05/09/2023]
Abstract
The liquorice genus, Glycyrrhiza L. (Leguminosae), is a medicinal herb with great economic importance and an intriguing intercontinental disjunct distribution in Eurasia, North Africa, the Americas, and Australia. Glycyrrhiza, along with Glycyrrhizopsis Boiss. and Meristotropis Fisch. & C.A.Mey., comprise Glycyrrhiza s.l. Here we reconstructed the phylogenetic relationships and biogeographic history in Glycyrrhiza s.l. using sequence data of whole chloroplast genomes. We found that Glycyrrhiza s.l. is sister to the tribe Wisterieae and is divided into four main clades. Clade I, corresponds to Glycyrrhizopsis and is sister to Glycyrrhiza sensu Meng. Meristotropis is embedded within Glycyrrhiza sensu Meng, and these two genera together form Clades II-IV. Based on biogeographic analyses and divergence time dating, Glycyrrhiza s.l. originated during the late Eocene and its most recent common ancestor (MRCA) was distributed in the interior of Eurasia and the circum-Mediterranean region. A vicariance event, which was possibly a response to the uplifting of the Turkish-Iranian Plateau, may have driven the divergence between Glycyrrhiza sensu Meng and Glycyrrhizopsis in the Middle Miocene. The third and fourth main uplift events of the Qinghai-Tibetan Plateau may have led to rapid evolutionary diversification within Glycyrrhiza sensu Meng. Subsequently, the MRCA of Clade II might have migrated to North America (G. lepidota) via the Bering land bridge during the early Pliocene, and reached temperate South America (G. astragalina) by long-distance dispersal (LDD). Within Clade III, the ancestor of G. acanthocarpa arrived at southern Australia through LDD after the late Pliocene, whereas all other species (the SPEY clade) migrated to the interior of Eurasia and the Mediterranean region in the early Pleistocene. The MRCA of Clade IV was restricted in the interior of Eurasia, but its descendants have become widespread in temperate regions of the Old World Northern Hemisphere during the last million years.
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Affiliation(s)
- Lei Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
- *Correspondence: Lei Duan,
| | - A.J. Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species in Southwest China, Kunming Institution of Botany, Chinese Academy of Sciences, Kunming, China
| | - Emine Arslan
- Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey
| | - Kuddisi Ertuğrul
- Department of Biology, Faculty of Science, Selçuk University, Konya, Turkey
| | - Phan Ke Loc
- Department of Botany and HNU, Faculty of Biology, VNU Hanoi University of Science (HUS), Hanoi, Vietnam
| | - Hiroaki Hayashi
- Laboratory of Natural Products Chemistry, College of Pharmaceutical Sciences, Ritsumeikan University, Kyoto, Japan
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
- Jun Wen,
| | - Hong-Feng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Hong-Feng Chen,
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