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Makhmudjanov D, Volis S, Yusupov Z, Juramurodov I, Tojibaev K, Deng T, Sun H. Central Asia revealed as a key area in evolution of Eremurus (Asphodelaceae). PLANT DIVERSITY 2024; 46:333-343. [PMID: 38798731 PMCID: PMC11119512 DOI: 10.1016/j.pld.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 05/29/2024]
Abstract
Eremurus was described at the beginning of the 19th century. However, due to limited sampling and the small number of gene markers to date, its phylogeny and evolution are largely unknown. In this study, we analyzed plastomes from 27 species belonging to 2 subgenera and 3 sections of Eremurus, which are found in Central Asia (its center of diversity) and China. We also analyzed nuclear DNA ITS of 33 species, encompassing all subgenera and sections of the genus in Central Asia, southwest Asia and China. Our findings revealed that the genus was monophyletic, although both subgenera Eremurus and Henningia were found to be paraphyletic. Both plastome and nrDNA-based phylogenetic trees had three clades that did not reflect the current taxonomy of the genus. Our biogeographical and time-calibrated trees suggest that Eremurus originated in the ancient Tethyan area in the second half of the Eocene. Diversification of Eremurus occurred from the early Oligocene to the late Miocene. Paratethys Sea retreat and several orogenetic events, such as the progressive uplift of the Qinghai-Tibet Plateau and surrounding mountain belts (Altai, Pamir, Tian Shan), caused serious topographic and climate (aridification) changes in Central Asia that may have triggered a split of clades and speciation. In this transformed Central Asia, speciation proceeded rapidly driven mainly by vicariance caused by numerous mountain chains and specialization to a variety of climatic, topographic and soil conditions that exist in this region.
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Affiliation(s)
- Dilmurod Makhmudjanov
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Sergei Volis
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Ziyoviddin Yusupov
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Inom Juramurodov
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Komiljon Tojibaev
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
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2
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Stubbins B, Leier AL, Barbeau DL, Pullen A, Abell JT, Nie J, Zárate MA, Fidler MK. Global climate forcing on late Miocene establishment of the Pampean aeolian system in South America. Nat Commun 2023; 14:6899. [PMID: 37899425 PMCID: PMC10613622 DOI: 10.1038/s41467-023-42537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Wind-blown dust from southern South America links the terrestrial, marine, atmospheric, and biological components of Earth's climate system. The Pampas of central Argentina (~33°-39° S) contain a Miocene to Holocene aeolian record that spans an important interval of global cooling. Upper Miocene sediment provenance based on n = 3299 detrital-zircon U-Pb ages is consistent with the provenance of Pleistocene-Holocene deposits, indicating the Pampas are the site of a long-lived fluvial-aeolian system that has been operating since the late Miocene. Here, we show the establishment of aeolian sedimentation in the Pampas coincided with late Miocene cooling. These findings, combined with those from the Chinese Loess Plateau (~33°-39° N) underscore: (1) the role of fluvial transport in the development and maintenance of temporally persistent mid-latitude loess provinces; and (2) a global-climate forcing mechanism behind the establishment of large mid-latitude loess provinces during the late Miocene.
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Affiliation(s)
- Blake Stubbins
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, 29208, USA
| | - Andrew L Leier
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, 29208, USA
| | - David L Barbeau
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC, 29208, USA
| | - Alex Pullen
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, 29634, USA.
| | - Jordan T Abell
- Department of Geosciences, University of Arizona, Tucson, AZ, 85721, USA
- Department of Earth and Environmental Sciences, Lehigh University, Pennsylvania, PA, 18015, USA
| | - Junsheng Nie
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Marcelo A Zárate
- Instituto de Ciencias de la Tierra y Ambientales de La Pampa, CONICET Universidad Nacional de La Pampa, La Pampa, Argentina
| | - Mary Kate Fidler
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, 29634, USA
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Bridges JD, Tarduno JA, Cottrell RD, Herbert TD. Rapid strengthening of westerlies accompanied intensification of Northern Hemisphere glaciation. Nat Commun 2023; 14:3905. [PMID: 37400450 DOI: 10.1038/s41467-023-39557-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
The trigger, pace, and nature of the intensification of Northern Hemisphere Glaciation (iNHG) are uncertain, but can be probed by study of ODP Site 1208 North Pacific marine sediments. Herein, we present magnetic proxy data that indicate a 4-fold increase of dust between ~ 2.73 and ~ 2.72 Ma, with subsequent increases at the start of glacials thereafter, indicating a strengthening of the mid-latitude westerlies. Moreover, a permanent shift in dust composition after 2.72 Ma is observed, consistent with drier conditions in the source region and/or the incorporation of material which could not have been transported via the weaker Pliocene winds. The sudden increase in our dust proxy data, a coeval rapid rise in dust recorded by proxy dust data in the North Atlantic (Site U1313), and the Site 1208 shift in dust composition, suggest that the iNHG represents a permanent crossing of a climate threshold toward global cooling and ice sheet growth, ultimately driven by lower atmospheric CO2.
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Affiliation(s)
- Joshua D Bridges
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA.
| | - John A Tarduno
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA.
- Department of Physics and Astronomy, University of Rochester, Rochester, NY, 14627, USA.
- Laboratory of Laser Energetics, University of Rochester, Rochester, NY, 14623, USA.
| | - Rory D Cottrell
- Department of Earth and Environmental Sciences, University of Rochester, Rochester, NY, 14627, USA
| | - Timothy D Herbert
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, 02912, USA
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Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae). Mol Phylogenet Evol 2023; 184:107808. [PMID: 37156329 DOI: 10.1016/j.ympev.2023.107808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30-24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12-23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.
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Affiliation(s)
- Qing-Hui Sun
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA; Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638, Munich, Germany
| | - Hong-Xin Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Zhai Mingguo Academician Work Station, Sanya University, Sanya 572022, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA; BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Hua-Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou 570228, China.
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5
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Wu N, Wang S, Dujsebayeva TN, Chen D, Ali A, Guo X. Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia. Mol Phylogenet Evol 2023; 184:107781. [PMID: 37044189 DOI: 10.1016/j.ympev.2023.107781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.
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Affiliation(s)
- Na Wu
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wang
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China
| | - Tatjana N Dujsebayeva
- Laboratory of Ornithology and Herpetology, Institute of Zoology, Ministry of Sciences and High Education of Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Abid Ali
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguang Guo
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China.
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6
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Jiang D, Liao L, Xing H, Chen Z, Luo X, Li HL. Interplay of Ecological Opportunities and Functional Traits Drives the Evolution and Diversification of Millettiod Legumes (Fabaceae). Genes (Basel) 2022; 13:genes13122220. [PMID: 36553487 PMCID: PMC9777679 DOI: 10.3390/genes13122220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Understanding the striking diversity of the angiosperms is a paramount issue in biology and of interest to biologists. The Millettiod legumes is one of the most hyper-diverse groups of the legume family, containing many economically important medicine, furniture and craft species. In the present study, we explore how the interplay of past climate change, ecological opportunities and functional traits' evolution may have triggered diversification of the Millettiod legumes. Using a comprehensive species-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that three dramatic accumulations of the Millettiod legumes occurred during the Miocene. The rapid diversification of the Millettiod legumes in the Miocene was driven by ecological opportunities created by the emergence of new niches and range expansion. Additionally, habit shifts and the switch between biomes might have facilitated the rapid diversification of the Millettiod legumes. The Millettiod legumes provide an excellent case for supporting the idea that the interplay of functional traits, biomes, and climatic and geographic factors drives evolutionary success.
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7
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Zhang H, Lu H, He J, Xie W, Wang H, Zhang H, Breecker D, Bird A, Stevens T, Nie J, Li G. Large-number detrital zircon U-Pb ages reveal global cooling caused the formation of the Chinese Loess Plateau during Late Miocene. SCIENCE ADVANCES 2022; 8:eabq2007. [PMID: 36223463 PMCID: PMC9555786 DOI: 10.1126/sciadv.abq2007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
The formation and evolution of the landscape of the Chinese Loess Plateau (CLP) is debated because of uncertainties regarding dust provenance. We present a quantitative estimation of dust source contributions to the CLP, based on more than 37,100 detrital zircon U-Pb ages, combined with mineral assemblages and isotope analyses. Our results reveal that the CLP was stepwise formed by ~8 million years (Ma) and is mainly composed of material from the Northeastern Qinghai-Tibetan Plateau, with stepwise shifts in relative contributions of different eolian silt sources occurring at ~2.6 Ma and 1.5 to 1.2 Ma. We infer that these changes were driven by stepwise global cooling, which induced aridification and enhanced silt production in glaciated-cold climate dust source regions, as well as dust ablation in the expanded arid regions. We propose that global cooling, rather than regional tectonic deformation, was the main driver of the formation and evolution of the CLP during late Cenozoic.
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Affiliation(s)
- Hanzhi Zhang
- Frontiers Science Center for Critical Earth Material Cycling, School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Huayu Lu
- Frontiers Science Center for Critical Earth Material Cycling, School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Jing He
- Frontiers Science Center for Critical Earth Material Cycling, School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Wanting Xie
- Frontiers Science Center for Critical Earth Material Cycling, School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Hanlin Wang
- Frontiers Science Center for Critical Earth Material Cycling, School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Hongyan Zhang
- Frontiers Science Center for Critical Earth Material Cycling, School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Daniel Breecker
- Department of Geological Sciences, University of Texas at Austin, Austin, TX 78712-1722, USA
| | - Anna Bird
- Department of Geography, Geology and Environment, University of Hull, Hull HU6 7RX, UK
| | - Thomas Stevens
- Department of Earth Sciences, Uppsala University, Villavägen 16, 752 36 Uppsala, Sweden
| | - Junsheng Nie
- MOE Key Laboratory of Western China’s Environmental Systems, Lanzhou University, Lanzhou 73000, China
| | - Gaojun Li
- Frontiers Science Center for Critical Earth Material Cycling, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
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Luo M, Jia H, Li Q, Meng X, Ferguson DK, Liu P, Han Z, Wang J, Quan C. Middle Miocene lotus (Nelumbonaceae, Nelumbo) from the Qaidam Basin, Northern Tibet Plateau. BIOLOGY 2022; 11:1261. [PMID: 36138740 PMCID: PMC9495916 DOI: 10.3390/biology11091261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
The Neogene environment and paleovegetation of today’s semi-arid and arid Central Asia remain elusive. Little is known about the effect of paleoclimatic change on the distribution and ecological response mechanisms of aquatic plants, especially on the Tibetan Plateau. Here, we report a new species of Nelumbo Adanson, including leaves, receptacles, and fruits, namely Nelumbo delinghaensis sp. nov., from the Upper Youshashan Formation of the upper Middle Miocene in the northern Qaidam Basin on the Tibetan Plateau. The new species comprises centrally peltate leaves with 12−15 actinodromous primary veins and a receptacle embedded with ca. 15−30 fruits, with an unlobed central disc. Megafossils of lotus from northwest China broaden the geographical and stratigraphic ranges of Nelumbo. Our findings suggest that a large freshwater lake body surrounded by temperate forests and grassland developed in the Qaidam Basin during the late Middle Miocene, in sharp contrast to the present desert vegetation. The climate used to be sufficiently warm and moist enough to support a forest-steppe ecosystem with abundant freshwater bodies.
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Affiliation(s)
- Mingyue Luo
- School of Earth Sciences and Engineering, Xi’an Shiyou University, Xi’an 710065, China
- Shaanxi Key Lab of Petroleum Accumulation Geology, Xi’an Shiyou University, Xi’an 710065, China
| | - Hui Jia
- School of Earth Sciences and Engineering, Xi’an Shiyou University, Xi’an 710065, China
- Shaanxi Key Lab of Petroleum Accumulation Geology, Xi’an Shiyou University, Xi’an 710065, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Nanjing 210008, China
| | - Qijia Li
- School of Earth Sciences and Resources, Chang’an University, Xi’an 710054, China
| | - Xiangning Meng
- School of Earth Sciences and Engineering, Xi’an Shiyou University, Xi’an 710065, China
- Shaanxi Key Lab of Petroleum Accumulation Geology, Xi’an Shiyou University, Xi’an 710065, China
| | - David K. Ferguson
- Department of Paleontology, University of Vienna, A-1090 Vienna, Austria
| | - Ping Liu
- School of Earth Sciences and Engineering, Xi’an Shiyou University, Xi’an 710065, China
- Shaanxi Key Lab of Petroleum Accumulation Geology, Xi’an Shiyou University, Xi’an 710065, China
| | - Zhuochen Han
- School of Earth Sciences and Engineering, Xi’an Shiyou University, Xi’an 710065, China
- Shaanxi Key Lab of Petroleum Accumulation Geology, Xi’an Shiyou University, Xi’an 710065, China
| | - Junjie Wang
- School of Earth Sciences and Engineering, Xi’an Shiyou University, Xi’an 710065, China
- Shaanxi Key Lab of Petroleum Accumulation Geology, Xi’an Shiyou University, Xi’an 710065, China
| | - Cheng Quan
- School of Earth Sciences and Resources, Chang’an University, Xi’an 710054, China
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9
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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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10
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Wang M, Zhang L, Tong S, Jiang D, Fu Z. Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. DNA Res 2022; 29:dsac006. [PMID: 35266513 PMCID: PMC8946665 DOI: 10.1093/dnares/dsac006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/09/2022] [Indexed: 01/30/2023] Open
Abstract
Haloxylon ammodendron is a xerophytic perennial shrub or small tree that has a high ecological value in anti-desertification due to its high tolerance to drought and salt stress. Here, we report a high-quality, chromosome-level genome assembly of H. ammodendron by integrating PacBio's high-fidelity sequencing and Hi-C technology. The assembled genome size was 685.4 Mb, of which 99.6% was assigned to nine pseudochromosomes with a contig N50 value of 23.6 Mb. Evolutionary analysis showed that both the recent substantial amplification of long terminal repeat retrotransposons and tandem gene duplication may have contributed to its genome size expansion and arid adaptation. An ample amount of low-GC genes was closely related to functions that may contribute to the desert adaptation of H. ammodendron. Gene family clustering together with gene expression analysis identified differentially expressed genes that may play important roles in the direct response of H. ammodendron to water-deficit stress. We also identified several genes possibly related to the degraded scaly leaves and well-developed root system of H. ammodendron. The reference-level genome assembly presented here will provide a valuable genomic resource for studying the genome evolution of xerophytic plants, as well as for further genetic breeding studies of H. ammodendron.
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Affiliation(s)
- Mingcheng Wang
- Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan 750001, China
| | - Shaofei Tong
- MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu 610105, China
| | - Dechun Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhixi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
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11
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Kong H, Condamine FL, Yang L, Harris AJ, Feng C, Wen F, Kang M. Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene. Syst Biol 2021; 71:589-609. [PMID: 34396416 PMCID: PMC9016594 DOI: 10.1093/sysbio/syab068] [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: 10/27/2020] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/02/2022] Open
Abstract
Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied the evolutionary radiation of Oreocharis (Gesneriaceae), which has diversified extensively throughout East Asia, especially within the Hengduan Mountains (HDM), using transcriptomic data and a time calibrated phylogeny for 88% (111/126) of all species of the genus. In particular, we applied phylogenetic reconstructions to evaluate the extent of incomplete lineage sorting accompanying the early and rapid radiation in the genus. We then fit macroevolutionary models to explore its spatial and diversification dynamics in Oreocharis and applied explicit birth–death models to investigate the effects of past environmental changes on its diversification. Evidence from 574 orthologous loci suggest that Oreocharis underwent an impressive early burst of speciation starting ca. 12 Ma in the Miocene, followed by a drastic decline in speciation toward the present. Although we found no evidence for a shift in diversification rate across the phylogeny of Oreocharis, we showed a difference in diversification dynamics between the HDM and non-HDM lineages, with higher diversification rates in the HDM. The diversification dynamic of Oreocharis is most likely positively associated with temperature-dependent speciation and dependency on the Asian monsoons. We suggest that the warm and humid climate of the mid-Miocene was probably the primary driver of the rapid diversification in Oreocharis, while mountain building of the HDM might have indirectly affected species diversification of the HDM lineage. This study highlights the importance of past climatic changes, combined with mountain building, in creating strong environmental heterogeneity and driving diversification of mountain plants, and suggests that the biodiversity in the HDM cannot directly be attributed to mountain uplift, contrary to many recent speculations.[East Asian monsoons; environmental heterogeneity; Hengduan Mountains; incomplete lineage sorting; Oreocharis; past climate change; rapid diversification; transcriptome.]
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Affiliation(s)
- Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Fang Wen
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, 541006 Guilin, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 510650 Guangzhou, China
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12
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Li X, Wu HX, Li J, Chen H, Wang W. The insights into the evolutionary history of Translucidithyrium: based on a newly-discovered species. MycoKeys 2020. [DOI: 10.3897/mycokeys.76.58628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the field studies, a Translucidithyrium-like taxon was collected in Xishuangbanna of Yunnan Province, during an investigation into the diversity of microfungi in the southwest of China. Morphological observations and phylogenetic analysis of combined LSU and ITS sequences revealed that the new taxon is a member of the genus Translucidithyrium and it is distinct from other species. Therefore, Translucidithyrium chinensesp. nov. is introduced here. The Maximum Clade Credibility (MCC) tree from LSU rDNA of Translucidithyrium and related species indicated the divergence time of existing and new species of Translucidithyrium was crown age at 16 (4–33) Mya. Combining the estimated divergence time, paleoecology and plate tectonic movements with the corresponding geological time scale, we proposed a hypothesis that the speciation (estimated divergence time) of T. chinense was earlier than T. thailandicum. Our findings provided new insights into the species of Translucidithyrium about ecological adaptation and speciation in two separate areas.
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13
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Wang Y, Lu H, Wang K, Wang Y, Li Y, Clemens S, Lv H, Huang Z, Wang H, Hu X, Lu F, Zhang H. Combined high- and low-latitude forcing of East Asian monsoon precipitation variability in the Pliocene warm period. SCIENCE ADVANCES 2020; 6:6/46/eabc2414. [PMID: 33188021 PMCID: PMC7673752 DOI: 10.1126/sciadv.abc2414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
East Asian monsoon variability in the Pliocene warm world has not been sufficiently studied because of the lack of direct records. We present a high-resolution precipitation record from Pliocene fluvial-lacustrine sequences in the Weihe Basin, Central China, a region sensitive to the East Asian monsoon. The record shows an abrupt monsoon shift at ~4.2 million years ago, interpreted as the result of high-latitude cooling, with an extratropical temperature decrease across a critical threshold. The precipitation time series exhibits a pronounced ~100-thousand year periodicity and the presence of precession and half-precession cycles, which suggest low-latitude forcing. The synchronous phase but mismatched amplitudes of the East Asian monsoon precipitation proxy and eccentricity suggest a nonlinear but sensitive precipitation response to temperature forcing in the Pliocene warm world. These observations highlight the role of high- and low-latitude forcing of East Asian monsoon variations on tectonic and orbital time scales.
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Affiliation(s)
- Yichao Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Huayu Lu
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China.
| | - Kexin Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Yao Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Yongxiang Li
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Steven Clemens
- Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - Hengzhi Lv
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Zihan Huang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Hanlin Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Xuzhi Hu
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Fuzhi Lu
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Hanzhi Zhang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
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14
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Li J, Han LH, Liu XB, Zhao ZW, Yang ZL. The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation. IMA Fungus 2020; 11:10. [PMID: 32617259 PMCID: PMC7325090 DOI: 10.1186/s43008-020-00031-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 12/02/2022] Open
Abstract
The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201 Yunnan China
- State Key Laboratory of Conservation and Utilization for Bioresources in Yunnan, Yunnan University, Kunming, 650091 Yunnan China
| | - Li-Hong Han
- College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, 655011 Yunnan China
| | - Xiao-Bin Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201 Yunnan China
| | - Zhi-Wei Zhao
- State Key Laboratory of Conservation and Utilization for Bioresources in Yunnan, Yunnan University, Kunming, 650091 Yunnan China
| | - Zhu L. Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201 Yunnan China
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15
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Wang H, Lu H, Zhao L, Zhang H, Lei F, Wang Y. Asian monsoon rainfall variation during the Pliocene forced by global temperature change. Nat Commun 2019; 10:5272. [PMID: 31754108 PMCID: PMC6872654 DOI: 10.1038/s41467-019-13338-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 11/04/2019] [Indexed: 11/15/2022] Open
Abstract
The Asian monsoon variations under global temperature changes during the Pliocene are still debated. Here we use a sedimentary record of phytoliths (plant silica) from the Weihe Basin, central China, to explore the history of C4 grasses and quantitatively reconstruct the Asian monsoon climate since the late Miocene. Our results show that C4 grasses have been a dominant grassland component since ~11.0 Ma. A subsequent marked decrease in warm- and humid-adapted C4 grasses and an increase in cool- and dry-adapted C3 grasses occurred in the Pliocene, ~4.0 Ma; the phytolith-based quantitative reconstruction of mean annual precipitation marked a decrease from 800~1673 mm to 443~900 mm, indicating a reduction in Asian monsoon rainfall in the Pliocene. Our newly obtained records conflict with the hypothesis that the growth of the Tibetan Plateau strengthened the Asian monsoon rainfall. Nevertheless, they emphasize the importance of global temperature as a determinant of Pliocene Asian monsoon variations. Asian summer monsoons and their links to global temperature changes have been the subject of intense debate. Here the authors reconstruct the Asian monsoon climate since the late Miocene, using plant silica records of C4 and C3 grasses in central China, and find that global cooling caused Asian monsoon rainfall to decrease markedly in the late Pliocene.
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Affiliation(s)
- Hanlin Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Huayu Lu
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China. .,Jiangsu Provincial Collaborative Innovation Centre of Climate Change, Nanjing, 210023, China.
| | - Lin Zhao
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Hongyan Zhang
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Fang Lei
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Yichao Wang
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
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16
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Liu J, Guo X, Chen D, Li J, Yue B, Zeng X. Diversification and historical demography of the rapid racerunner (Eremias velox) in relation to geological history and Pleistocene climatic oscillations in arid Central Asia. Mol Phylogenet Evol 2019; 130:244-258. [DOI: 10.1016/j.ympev.2018.10.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
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17
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Global cooling and enhanced Eocene Asian mid-latitude interior aridity. Nat Commun 2018; 9:3026. [PMID: 30072688 PMCID: PMC6072711 DOI: 10.1038/s41467-018-05415-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/02/2018] [Indexed: 11/25/2022] Open
Abstract
Tibetan Plateau uplift has been suggested as the main driving force for mid-latitude Asian inland aridity (AIA) and for deposition of thick aeolian sequences in northern China since the Miocene. However, the relationship between earlier AIA and Tibetan Plateau mountain building is uncertain because of a lack of corresponding thick aeolian sequences with accurate age constraints. We here present results for a continuous aeolian sequence that spans the interval from >51 to 39 Ma from the eastern Xorkol Basin, Altun Shan, northeastern Tibetan Plateau. The basal age of the studied sequence postdates initial uplift of the Tibetan Plateau by several million years. Our results indicate that the local palaeoclimate was teleconnected strongly to the overall global cooling pattern, so that local enhanced aridification recorded by the studied aeolian sequence is dominantly a response to global climatic forcing rather than plateau uplift. The role Tibetan Plateau uplift played in Asian inland aridification remains unclear due to a paucity of accurately dated records. Here, the authors present a continuous aeolian sequence for the period >51–39 Ma, analysis of which indicates that aridification was driven by global climatic forcing rather than uplift.
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18
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Kong H, Condamine FL, Harris AJ, Chen J, Pan B, Möller M, Hoang VS, Kang M. Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China. Mol Ecol 2017; 26:6414-6429. [PMID: 28960701 DOI: 10.1111/mec.14367] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 01/19/2023]
Abstract
Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to palaeoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid-Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat.
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Affiliation(s)
- Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Montpellier, France
| | - A J Harris
- Department of Botany, MRC 166, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Junlin Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Bo Pan
- Guangxi Institute of Botany, Guangxi Zhang Autonomous Region and the Chinese Academy of Sciences, Guilin, China
| | | | - Van Sam Hoang
- Forest Plant Department, Vietnam National University of Forestry, Hanoi, Vietnam
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw, Myanmar
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19
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Consistent C3 plant habitat of hominins during 400–300 ka at the Longyadong Cave site (Luonan Basin, central China) revealed by stable carbon isotope analyses of loess deposits. J Hum Evol 2017. [DOI: 10.1016/j.jhevol.2017.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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20
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Qian C, Yin H, Shi Y, Zhao J, Yin C, Luo W, Dong Z, Chen G, Yan X, Wang XR, Ma XF. Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change. Sci Rep 2016; 6:26613. [PMID: 27210568 PMCID: PMC4876407 DOI: 10.1038/srep26613] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/04/2016] [Indexed: 12/02/2022] Open
Abstract
Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since ~1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.
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Affiliation(s)
- Chaoju Qian
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hengxia Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Shi
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiecai Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengliang Yin
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyin Luo
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Zhibao Dong
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xia Yan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
- Key Laboratory of Eco-hydrology and of Inland River Basin, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå 90187, Sweden
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Department of Ecology and Agriculture Research, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, Gansu, China
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21
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Wu SD, Lin L, Li HL, Yu SX, Zhang LJ, Wang W. Evolution of Asian Interior Arid-Zone Biota: Evidence from the Diversification of Asian Zygophyllum (Zygophyllaceae). PLoS One 2015; 10:e0138697. [PMID: 26393796 PMCID: PMC4579068 DOI: 10.1371/journal.pone.0138697] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/02/2015] [Indexed: 01/18/2023] Open
Abstract
The Asian interior arid zone is the largest desert landform system in the Northern Hemisphere, and has high biodiversity. Little is currently known about the evolutionary history of its biota. In this study, we used Zygophyllum, an important and characteristic component of the Asian interior arid zone, to provide new insights into the evolution of this biota. By greatly enlarged taxon sampling, we present the phylogenetic analysis of Asian Zygophyllum based on two plastid and one nuclear markers. Our phylogenetic analyses indicate that Asian Zygophyllum and Sarcozygium form a clade and Sarcozygium is further embedded within the shrub subclade. An integration of phylogenetic, biogeographic, and molecular dating methods indicates that Zygophyllum successfully colonized the Asian interior from Africa in the early Oligocene, and Asian Zygophyllum became differentiated in the early Miocene and underwent a burst of diversification in the late Miocene associated with the expansion of Asian interior arid lands due to orogenetic and climatic changes. Combining diversification patterns of other important components of the Asian interior arid zone, we propose a multi-stage evolution model for this biota: the late Eocene-early Oligocene origin, the early Miocene expansion, and the middle-late Miocene rapid expansion to the whole Asian interior arid zone. This study also demonstrates that, for Zygophyllum and perhaps other arid-adapted organisms, arid biomes are evolutionary cradles of diversity.
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Affiliation(s)
- Sheng-Dan Wu
- College of Life Sciences, Shanxi Normal University, Linfen, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Li Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Lei Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Sheng-Xiang Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lin-Jing Zhang
- College of Life Sciences, Shanxi Normal University, Linfen, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Le M, Nguyen HM, Duong HT, Nguyen TV, Dinh LD, Nguyen NX, Nguyen LD, Dinh TH, Nguyen DX. Phylogeography of the Laotian Rock Rat (Diatomyidae:Laonastes): Implications for Lazarus Taxa. MAMMAL STUDY 2015. [DOI: 10.3106/041.040.0206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Li Y, Song Y, Yan L, Chen T, An Z. Timing and Spatial Distribution of Loess in Xinjiang, NW China. PLoS One 2015; 10:e0125492. [PMID: 25970617 PMCID: PMC4430276 DOI: 10.1371/journal.pone.0125492] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 02/08/2015] [Indexed: 11/19/2022] Open
Abstract
Central Asia is one of the most significant loess regions on Earth, with an important role in understanding Quaternary climate and environmental change. However, in contrast to the widely investigated loess deposits in the Chinese Loess Plateau, the Central Asian loess–paleosol sequences are still insufficiently known and poorly understood. Through field investigation and review of the previous literature, the authors have investigated the distribution, thickness and age of the Xinjiang loess, and analyzed factors that control these parameters in the Xinjiang in northwest China, Central Asia. The loess sediments cover river terraces, low uplands, the margins of deserts and the slopes of the Tianshan Mountains and Kunlun Mountains and are also present in the Ili Basin. The thickness of the Xinjiang loess deposits varies from several meters to 670 m. The variation trend of the sand fraction (>63 μm) grain-size contour can indicate the local major wind directions, so we conclude that the NW and NE winds are the main wind directions in the North and South Xinjiang, and the westerly wind mainly transport dust into the Ili basin. We consider persistent drying, adequate regional wind energy and well-developed river terraces to be the main factors controlling the distribution, thickness and formation age of the Xinjiang loess. The well-outcropped loess sections have mainly developed since the middle Pleistocene in Xinjiang, reflecting the appearance of the persistent drying and the present air circulation system. However, the oldest loess deposits are as old as the beginning of the Pliocene in the Tarim Basin, which suggests that earlier aridification occurred in the Tarim Basin rather than in the Ili Basin and the Junggar Basin.
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Affiliation(s)
- Yun Li
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061, China
| | - Yougui Song
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061, China
- Joint Center for Global Change Studies, Beijing 100875, China
- * E-mail:
| | - Libin Yan
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061, China
| | - Tao Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061, 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 X, Dong B. Influence of the Tibetan Plateau uplift on the Asian monsoon-arid environment evolution. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5987-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lu H, Yi S, Xu Z, Zhou Y, Zeng L, Zhu F, Feng H, Dong L, Zhuo H, Yu K, Mason J, Wang X, Chen Y, Lu Q, Wu B, Dong Z, Qu J, Wang X, Guo Z. Chinese deserts and sand fields in Last Glacial Maximum and Holocene Optimum. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5919-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Dong X, Ding Z, Yang S, Luo P, Wang X, Ji J. Synchronous drying and cooling in central Asia during late Oligocene. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-5821-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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