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Hofmann S, Rödder D, Andermann T, Matschiner M, Riedel J, Baniya CB, Flecks M, Yang J, Jiang K, Jianping J, Litvinchuk SN, Martin S, Masroor R, Nothnagel M, Vershinin V, Zheng Y, Jablonski D, Schmidt J, Podsiadlowski L. Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae). Mol Ecol 2024; 33:e17446. [PMID: 38946613 DOI: 10.1111/mec.17446] [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: 03/06/2024] [Revised: 05/25/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.
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Affiliation(s)
- Sylvia Hofmann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Dennis Rödder
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Tobias Andermann
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Jendrian Riedel
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, Kathmandu, Nepal
| | - Morris Flecks
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Jianhuan Yang
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hong Kong, China
| | - Ke Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Jianping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | | | - Michael Nothnagel
- Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Vladimir Vershinin
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Institute of Natural Sciences and Mathematics, Eltsyn Ural Federal University, Yekaterinburg, Russia
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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Shi YJ, Mi JX, Huang JL, Tian FF, He F, Zhong Y, Yang HB, Wang F, Xiao Y, Yang LK, Zhang F, Chen LH, Wan XQ. A new species of Populus and the extensive hybrid speciation arising from it on the Qinghai-Tibet Plateau. Mol Phylogenet Evol 2024; 196:108072. [PMID: 38615706 DOI: 10.1016/j.ympev.2024.108072] [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: 10/10/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
While the diversity of species formation is broadly acknowledged, significant debate exists regarding the universal nature of hybrid species formation. Through an 18-year comprehensive study of all Populus species on the Qinghai-Tibet Plateau, 23 previously recorded species and 8 new species were identified. Based on morphological characteristics, these can be classified into three groups: species in section Leucoides, species with large leaves, and species with small leaves in section Tacamahaca. By conducting whole-genome re-sequencing of 150 genotypes from these 31 species, 2.28 million single nucleotide polymorphisms (SNPs) were identified. Phylogenetic analysis utilizing these SNPs not only revealed a highly intricate evolutionary network within the large-leaf species of section Tacamahaca but also confirmed that a new species, P. curviserrata, naturally hybridized with P. cathayana, P. szechuanica, and P. ciliata, resulting in 11 hybrid species. These findings indicate the widespread occurrence of hybrid species formation within this genus, with hybridization serving as a key evolutionary mechanism for Populus on the plateau. A novel hypothesis, "Hybrid Species Exterminating Their Ancestral Species (HSEAS)," is introduced to explain the mechanisms of hybrid species formation at three different scales: the entire plateau, the southeastern mountain region, and individual river valleys.
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Affiliation(s)
- Yu-Jie Shi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China
| | - Jia-Xuan Mi
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin-Liang Huang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fei-Fei Tian
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fang He
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Zhong
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China
| | - Han-Bo Yang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China
| | - Fang Wang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Xiao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin-Kai Yang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fan Zhang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang-Hua Chen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China
| | - Xue Qin Wan
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Province Key Laboratory of Ecological Forestry Engineering On the Upper Reaches of the Yangtze River, China.
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Zhang X, Guo S, Yuan B, Mu H, Xia Z, Tang P, Fang H, Wang Z, Du P. Error-Reduced Digital Elevation Model of the Qinghai-Tibet Plateau using ICESat-2 and Fusion Model. Sci Data 2024; 11:588. [PMID: 38839786 PMCID: PMC11153629 DOI: 10.1038/s41597-024-03428-4] [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: 12/14/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
The Qinghai-Tibet Plateau (QTP) holds significance for investigating Earth's surface processes. However, due to rugged terrain, forest canopy, and snow accumulation, open-access Digital Elevation Models (DEMs) exhibit considerable noise, resulting in low accuracy and pronounced data inconsistency. Furthermore, the glacier regions within the QTP undergo substantial changes, necessitating updates. This study employs a fusion of open-access DEMs and high-accuracy photons from the Ice, Cloud, and land Elevation Satellite-2 (ICESat-2). Additionally, snow cover and canopy heights are considered, and an ensemble learning fusion model is presented to harness the complementary information in the multi-sensor elevation observations. This innovative approach results in the creation of HQTP30, the most accurate representation of the 2021 QTP terrain. Comparative analysis with high-resolution imagery, UAV-derived DEMs, control points, and ICESat-2 highlights the advantages of HQTP30. Notably, in non-glacier regions, HQTP30 achieved a Mean Absolute Error (MAE) of 0.71 m, while in glacier regions, it reduced the MAE by 4.35 m compared to the state-of-the-art Copernicus DEM (COPDEM), demonstrating its versatile applicability.
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Affiliation(s)
- Xingang Zhang
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Shanchuan Guo
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China.
| | - Bo Yuan
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Haowei Mu
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Zilong Xia
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Pengfei Tang
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Hong Fang
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Zhuo Wang
- School of Resource and Environmental Sciences, Wuhan University, Wuhan, China
- Faculty of Geomatics, Lanzhou Jiaotong University, Lanzhou, China
| | - Peijun Du
- Key Laboratory for Land Satellite Remote Sensing Applications of Ministry of Natural Resources, Jiangsu Provincial Key Laboratory of Geographic Information Science and Technology, School of Geography and Ocean Science, Nanjing University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
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Rana SK, Rana HK, Landis JB, Kuang T, Chen J, Wang H, Deng T, Davis CC, Sun H. Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme L. in a major biodiversity hotspot. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1192-1205. [PMID: 38639466 DOI: 10.1111/jipb.13663] [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: 01/23/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer-scale population-level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco-morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67-0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming-cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts.
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Affiliation(s)
- Santosh Kumar Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, 72401, Arkansas, USA
| | - Hum Kala Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, 14853, New York, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, 14853, New York, USA
| | - Tianhui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Juntong Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Herbaria, Harvard University, Cambridge, 02138, Massachusetts, USA
| | - Hang Sun
- 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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Chen H, Li T, Chen X, Qu T, Zheng X, Luo J, Li B, Zhang G, Fu Z. Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome. FRONTIERS IN PLANT SCIENCE 2024; 15:1367132. [PMID: 38736446 PMCID: PMC11082289 DOI: 10.3389/fpls.2024.1367132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/25/2024] [Indexed: 05/14/2024]
Abstract
Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045-152,729 bp in length and contained 132-133 genes, including 87 protein-coding genes, 37-38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.
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Affiliation(s)
- Hui Chen
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Tingyu Li
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Xinyu Chen
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Tianmeng Qu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Xinyi Zheng
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Junjia Luo
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
| | - Bo Li
- Sichuan Environmental Monitoring Center, Chengdu, China
| | - Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zhixi Fu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, China
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Zhu H, Tan Y. The Origin of Evergreen Broad-Leaved Forests in East Asia from the Evidence of Floristic Elements. PLANTS (BASEL, SWITZERLAND) 2024; 13:1106. [PMID: 38674515 PMCID: PMC11054231 DOI: 10.3390/plants13081106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Arguments about the origin and evolution of the evergreen broad-leaved forests in East Asia exist generally, and are even contradictory in some cases. The origin and evolution of the flora of East Asia, especially in the evolutionary process, the formation time of the Asian monsoon, the implications of phylogenetic and biogeographic studies on some important taxa, and the implications of palaeobotanical evidence are debatable. Most research from different disciplines suggests that the monsoon in the Miocene was key to the diversification of East Asian flora and its evergreen broad-leaved forests. The common view is that the evergreen broad-leaved forests of East Asia are closely related to the monsoon's intensity and developments, which were caused by the uplift of Himalaya-Tibet during or after the mid-Miocene. Analysis of the floristic elements show that the present subtropical evergreen broad-leaved forests in East Asia could have an early or ancient tropical origin and a tropical Asian affinity, but that their species are dominated by endemic Chinese or East Asian ones, many of which have tropical Asian affinity or are tropical sister species. The time of Himalayan uplift and the intensity of the monsoon climate are believed to be key to the formation of the evergreen broad-leaved forests in East Asia. Combined with existing paleobotanical findings, the uplift of the Himalayas and the formation of the monsoon climate, as well as floristic elements of the subtropical evergreen broad-leaved forests, we believe that they evolved from an Asian tropical rainforest after the mid-Miocene in the southeastern region of East Asia, while the ancient subtropical evergreen broad-leaved forests in the southwestern region continuously evolved into the present subtropical ones.
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Affiliation(s)
- Hua Zhu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Mengla 666303, China;
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Shen X, Zong W, Li Y, Liu X, Zhuge F, Zhou Q, Zhou S, Jiang D. Evolution of Cherries ( Prunus Subgenus Cerasus) Based on Chloroplast Genomes. Int J Mol Sci 2023; 24:15612. [PMID: 37958595 PMCID: PMC10650623 DOI: 10.3390/ijms242115612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai-Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing-Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry's genetic resources.
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Affiliation(s)
- Xin Shen
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Wenjin Zong
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Yingang Li
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Xinhong Liu
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Fei Zhuge
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Qi Zhou
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dongyue Jiang
- Institute of Tree Breeding, Zhejiang Academy of Forestry, 399 Liuhe Road, Hangzhou 310023, China; (X.S.); (W.Z.); (Y.L.); (X.L.); (F.Z.); (Q.Z.)
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Yang L, Zhou G. Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations. BMC PLANT BIOLOGY 2023; 23:450. [PMID: 37749488 PMCID: PMC10521563 DOI: 10.1186/s12870-023-04471-w] [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: 08/20/2022] [Accepted: 09/17/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Climate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles. METHODS In this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera. RESULTS The genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding. CONCLUSION Our study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Guoying Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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Schmidt J, Opgenoorth L, Mao K, Baniya CB, Hofmann S. Molecular phylogeny of mega-diverse Carabus attests late Miocene evolution of alpine environments in the Himalayan-Tibetan Orogen. Sci Rep 2023; 13:13272. [PMID: 37582802 PMCID: PMC10427656 DOI: 10.1038/s41598-023-38999-6] [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: 10/21/2022] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
The timing, sequence, and scale of uplift of the Himalayan-Tibetan Orogen (HTO) are controversially debated. Many geoscientific studies assume paleoelevations close to present-day elevations and the existence of alpine environments across the HTO already in the late Paleogene, contradicting fossil data. Using molecular genetic data of ground beetles, we aim to reconstruct the paleoenvironmental history of the HTO, focusing on its southern margin (Himalayas, South Tibet). Based on a comprehensive sampling of extratropical Carabus, and ~ 10,000 bp of mitochondrial and nuclear DNA we applied Bayesian and Maximum likelihood methods to infer the phylogenetic relationships. We show that Carabus arrived in the HTO at the Oligocene-Miocene boundary. During the early Miocene, five lineages diversified in different parts of the HTO, initially in its southern center and on its eastern margin. Evolution of alpine taxa occurred during the late Miocene. There were apparently no habitats for Carabus before the late Oligocene. Until the Late Oligocene elevations must have been low throughout the HTO. Temperate forests emerged in South Tibet in the late Oligocene at the earliest. Alpine environments developed in the HTO from the late Miocene and, in large scale, during the Pliocene-Quaternary. Findings are consistent with fossil records but contrast with uplift models recovered from stable isotope paleoaltimetry.
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Affiliation(s)
- Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, 18055, Rostock, Germany.
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Faculty of Biology, Philipps-University Marburg, 35043, Marburg, Germany.
| | - Kangshan Mao
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, 44600, Kirtipur, Nepal
| | - Sylvia Hofmann
- Department Conservation Biology, UFZ-Helmholtz-Centre for Environmental Research GmbH, 04318, Leipzig, Germany.
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, 53113, Bonn, Germany.
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10
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Qi XG, Wu J, Zhao L, Wang L, Guang X, Garber PA, Opie C, Yuan Y, Diao R, Li G, Wang K, Pan R, Ji W, Sun H, Huang ZP, Xu C, Witarto AB, Jia R, Zhang C, Deng C, Qiu Q, Zhang G, Grueter CC, Wu D, Li B. Adaptations to a cold climate promoted social evolution in Asian colobine primates. Science 2023; 380:eabl8621. [PMID: 37262163 DOI: 10.1126/science.abl8621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 07/06/2022] [Indexed: 06/03/2023]
Abstract
The biological mechanisms that underpin primate social evolution remain poorly understood. Asian colobines display a range of social organizations, which makes them good models for investigating social evolution. By integrating ecological, geological, fossil, behavioral, and genomic analyses, we found that colobine primates that inhabit colder environments tend to live in larger, more complex groups. Specifically, glacial periods during the past 6 million years promoted the selection of genes involved in cold-related energy metabolism and neurohormonal regulation. More-efficient dopamine and oxytocin pathways developed in odd-nosed monkeys, which may have favored the prolongation of maternal care and lactation, increasing infant survival in cold environments. These adaptive changes appear to have strengthened interindividual affiliation, increased male-male tolerance, and facilitated the stepwise aggregation from independent one-male groups to large multilevel societies.
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Affiliation(s)
- Xiao-Guang Qi
- College of Life Sciences, Northwest University, Xi'an, China
| | - Jinwei Wu
- College of Life Sciences, Northwest University, Xi'an, China
| | - Lan Zhao
- College of Life Sciences, Northwest University, Xi'an, China
| | - Lu Wang
- College of Life Sciences, Northwest University, Xi'an, China
| | | | - Paul A Garber
- Department of Anthropology, University of Illinois, Urbana, IL, USA
| | - Christopher Opie
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Yuan Yuan
- College of Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Kun Wang
- College of Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Ruliang Pan
- College of Life Sciences, Northwest University, Xi'an, China
| | - Weihong Ji
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | | | - Zhi-Pang Huang
- College of Life Sciences, Northwest University, Xi'an, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Shanghai, China
| | - Arief B Witarto
- Faculty of Medicine, Universitas Pertahanan, Jabodetabek, Indonesia
| | - Rui Jia
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | | | - Cheng Deng
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiang Qiu
- College of Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Guojie Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Dongdong Wu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Baoguo Li
- College of Life Sciences, Northwest University, Xi'an, China
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11
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Xu T, Wang R, La Q, Yonezawa T, Huang X, Sun K, Song Z, Wang Y, Bartish IV, Zhang W, Cheng S. Climate heterogeneity shapes phylogeographic pattern of Hippophae gyantsensis (Elaeagnaceae) in the east Himalaya-Hengduan Mountains. Ecol Evol 2023; 13:e10182. [PMID: 37304372 PMCID: PMC10251425 DOI: 10.1002/ece3.10182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023] Open
Abstract
The interaction of recent orographic uplift and climate heterogeneity acted as a key role in the East Himalaya-Hengduan Mountains (EHHM) has been reported in many studies. However, how exactly the interaction promotes clade diversification remains poorly understood. In this study, we both used the chloroplast trnT-trnF region and 11 nuclear microsatellite loci to investigate the phylogeographic structure and population dynamics of Hippophae gyantsensis and estimate what role geological barriers or ecological factors play in the spatial genetic structure. The results showed that this species had a strong east-west phylogeographic structure, with several mixed populations identified from microsatellite data in central location. The intraspecies divergence time was estimated to be about 3.59 Ma, corresponding well with the recent uplift of the Tibetan Plateau. Between the two lineages, there was significant climatic differentiation without geographic barriers. High consistency between lineage divergence, climatic heterogeneity, and Qingzang Movement demonstrated that climatic heterogeneity but not geographic isolation drives the divergence of H. gyantsensis, and the recent regional uplift of the QTP, as the Himalayas, creates heterogeneous climates by affecting the flow of the Indian monsoon. The east group of H. gyantsensis experienced population expansion c. 0.12 Ma, closely associated with the last interglacial interval. Subsequently, a genetic admixture event between east and west groups happened at 26.90 ka, a period corresponding to the warm inter-glaciation again. These findings highlight the importance of the Quaternary climatic fluctuations in the recent evolutionary history of H. gyantsensis. Our study will improve the understanding of the history and mechanisms of biodiversity accumulation in the EHHM region.
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Affiliation(s)
- Ting Xu
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Ruixue Wang
- College of Life SciencesNorthwest Normal UniversityLanzhouChina
| | - Qiong La
- Department of BiologyTibet UniversityLhasaChina
| | - Takahiro Yonezawa
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Xinyi Huang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Kun Sun
- College of Life SciencesNorthwest Normal UniversityLanzhouChina
| | - Zhiping Song
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Yuguo Wang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Igor V. Bartish
- Institute of Botany of the Czech Academy of SciencesPruhoniceCzech Republic
| | - Wenju Zhang
- Institute of Biodiversity Science, School of Life SciencesFudan UniversityShanghaiChina
| | - Shanmei Cheng
- Laboratory of Subtropical BiodiversityJiangxi Agricultural UniversityNanchangChina
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12
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Zhai Y, Zhang T, Guo Y, Gao C, Zhou L, Feng L, Zhou T, Xumei W. Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes. JOURNAL OF PLANT RESEARCH 2023; 136:291-304. [PMID: 36808315 DOI: 10.1007/s10265-023-01440-0] [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: 10/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
As a traditional Chinese medicine, rhubarb is used to treat several diseases such as severe acute pancreatitis, sepsis and chronic renal failure. However, few studies focused on the authentication of germplasm for the Rheum palmatum complex, and no studies have been conducted to elucidate the evolutionary history of the R. palmatum complex using plastome datasets. Hence, we aim to develop the potential molecular markers to identify the elite germplasms of rhubarb and explore the divergence and biogeographic history of the R. palmatum complex based on the newly sequenced chloroplast genome datasets. Chloroplast genomes of thirty-five the R. palmatum complex germplasms were sequenced, and the length ranged from 160,858 to 161,204 bp. The structure, gene content and gene order were highly conserved across all genomes. Eight InDels and sixty-one SNPs loci could be used to authenticate the high-quality germplasms of rhubarb in specific areas. Phylogenetic analysis revealed that all rhubarb germplasms were clustered in the same clade with high bootstrap support values and Bayesian posterior probabilities. According to the molecular dating result, the intraspecific divergence of the complex occurred in the Quaternary, which might be affected by climatic fluctuation. The biogeography reconstruction indicated that the ancestor of the R. palmatum complex might originate from the Himalaya-Hengduan Mountains or/and Bashan-Qinling Mountains, and then spread to surrounding areas. Several useful molecular markers were developed to identify rhubarb germplasms, and our study will provide further understanding on speciation, divergence and biogeography of the R. palmatum complex.
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Affiliation(s)
- Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanbing Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Wang Xumei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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13
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Wu SS, Jiang MT, Miao JL, Li MH, Wang JY, Shen LM, Peng DH, Lan SR, Zhai JW, Liu ZJ. Origin and diversification of a Himalayan orchid genus Pleione. Mol Phylogenet Evol 2023; 184:107797. [PMID: 37086913 DOI: 10.1016/j.ympev.2023.107797] [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: 02/20/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023]
Abstract
Pleione is an orchid endemically distributed in high mountain areas across the Hengduan Mountains (HDM), Himalayas, Southeast Asia and South of China. The unique flower shapes, rich colors and immense medicinal importance of Pleione are valuable ornamental and economic resources. However, the phylogenetic relationships and evolutionary history of the genus have not yet been comprehensively resolved. Here, the evolutionary history of Pleione was investigated using single-copy gene single nucleotide polymorphisms and chloroplast genome datasets. The data revealed that Pleione could be divided into five clades. Discordance in topology between the two phylogenetic trees and network and D-statistic analyses indicated the occurrence of reticulate evolution in the genus. The evolution could be attributed to introgression and incomplete lineage sorting. Ancestral area reconstruction suggested that Pleione was originated from the HDM. Uplifting of the HDM drove rapid diversification by creating conditions favoring rapid speciation. This coincided with two periods of consolidation of the Asian monsoon climate, which caused the first rapid diversification of Pleione from 8.87 to 7.83 Mya, and a second rapid diversification started at around 4.05 Mya to Pleistocene. The interaction between Pleione and climate changes, especially the monsoons, led to the current distribution pattern and shaped the dormancy characteristic of the different clades. In addition to revealing the evolutionary relationship of Pleione with orogeny and climate changes, the findings of this study provide insights into the speciation and diversification mechanisms of plants in the East Asian flora.
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Affiliation(s)
- Sha-Sha Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-Tao Jiang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiang-Lin Miao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie-Yu Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Li-Ming Shen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jun-Wen Zhai
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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14
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Yao Z, Shi X, Guo Z, Li X, Nath BN, Betzler C, Zhang H, Lindhorst S, Miriyala P. Weakening of the South Asian summer monsoon linked to interhemispheric ice-sheet growth since 12 Ma. Nat Commun 2023; 14:829. [PMID: 36788217 PMCID: PMC9929083 DOI: 10.1038/s41467-023-36537-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
The evolution and driving mechanism of the South Asian summer monsoon (SASM) are still poorly understood. We here present a 12-Myr long SASM record by analyzing the strontium and neodymium isotopic composition of detrital components at IODP Exp. 359 Site U1467 from the northern Indian Ocean. The provenance investigation demonstrates that more dust enriched in εNd from northeastern Africa and the Arabian Peninsula was transported to the study site by monsoonal and Shamal winds during the summer monsoon season. A two-step weakening of the SASM wind since ~12 Ma is proposed based on the εNd record. This observational phenomenon is supported by climate modeling results, demonstrating that the SASM evolution was mainly controlled by variations in the gradient between the Mascarene High and the Indian Low, associated with meridional shifts of the Hadley Cell and the Intertropical Convergence Zone, which were caused by interhemispheric ice-sheet growth since the Middle Miocene.
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Affiliation(s)
- Zhengquan Yao
- Key Laboratory of Marine Geology and Metallogeny, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China. .,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Xuefa Shi
- Key Laboratory of Marine Geology and Metallogeny, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China. .,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhengtang Guo
- grid.9227.e0000000119573309Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309CAS Center for Excellence in Life and Paleoenvironment, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinzhou Li
- grid.9227.e0000000119573309State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, China ,grid.458457.f0000 0004 1792 8067CAS Center for Excellence in Quaternary Science and Global Change, Xi’an, China
| | - B. Nagender Nath
- grid.436330.10000 0000 9040 9555Geological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa India
| | - Christian Betzler
- grid.9026.d0000 0001 2287 2617Institute of Geology, CEN, University of Hamburg, Hamburg, Germany
| | - Hui Zhang
- grid.453137.70000 0004 0406 0561Key Laboratory of Marine Geology and Metallogeny, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Sebastian Lindhorst
- grid.9026.d0000 0001 2287 2617Institute of Geology, CEN, University of Hamburg, Hamburg, Germany
| | - Pavan Miriyala
- grid.419382.50000 0004 0496 9708CSIR-National Geophysical Research Institute, Hyderabad, India
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15
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Miao Y, Fang X, Sun J, Xiao W, Yang Y, Wang X, Farnsworth A, Huang K, Ren Y, Wu F, Qiao Q, Zhang W, Meng Q, Yan X, Zheng Z, Song C, Utescher T. A new biologic paleoaltimetry indicating Late Miocene rapid uplift of northern Tibet Plateau. Science 2022; 378:1074-1079. [DOI: 10.1126/science.abo2475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The uplift of the Tibet Plateau (TP) during the Miocene is crucial to understanding the evolution of Asian monsoon regimes and alpine biodiversity. However, the northern Tibet Plateau (NTP) remains poorly investigated. We use pollen records of montane conifers (
Tsuga
,
Podocarpus
,
Abies
, and
Picea
) as a new paleoaltimetry to construct two parallel midrange paleoelevation sequences in the NTP at 1332 ± 189 m and 433 ± 189 m, respectively, during the Middle Miocene [~15 million years ago (Ma)]. Both midranges increased rapidly to 3685 ± 87 m in the Late Miocene (~11 Ma) in the east, and to 3589 ± 62 m at ~7 Ma in the west. Our estimated rises in the east and west parts of the NTP during 15 to 7 Ma, together with data from other TP regions, indicate that during the Late Miocene the entire plateau may have reached a high elevation close to that of today, with consequent impacts on atmospheric precipitation and alpine biodiversity.
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Affiliation(s)
- Yunfa Miao
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- National Key Laboratory of Arid Area Ecological Security and Sustainable Development, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Tibetan Plateau Earth System Science, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaomin Fang
- State Key Laboratory of Tibetan Plateau Earth System Science, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jimin Sun
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Wenjiao Xiao
- National Key Laboratory of Arid Area Ecological Security and Sustainable Development, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Research Center for Mineral Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Yongheng Yang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- National Key Laboratory of Arid Area Ecological Security and Sustainable Development, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xuelian Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- National Key Laboratory of Arid Area Ecological Security and Sustainable Development, Chinese Academy of Sciences, Urumqi 830011, China
| | - Alex Farnsworth
- State Key Laboratory of Tibetan Plateau Earth System Science, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- School of Geographical Sciences and Cabot Institute, University of Bristol, Bristol BS8 1SS, UK
| | - Kangyou Huang
- Guangdong Provincial Key Laboratory of Geodynamics and Geohazards, School of Earth Sciences and Engineering, Sun Yat-sen University, Zhuhai 519082, China
| | - Yulong Ren
- Key Laboratory of Arid Climate Change and Disaster Reduction of CMA and of Gansu Province, Institute of Arid Meteorology, Lanzhou 730000, China
| | - Fuli Wu
- State Key Laboratory of Tibetan Plateau Earth System Science, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingqing Qiao
- National Key Laboratory of Arid Area Ecological Security and Sustainable Development, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Research Center for Mineral Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Weilin Zhang
- State Key Laboratory of Tibetan Plateau Earth System Science, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingquan Meng
- School of Earth Sciences and Key Laboratory of Mineral Resources in Western China (Gansu Province), Lanzhou University, Lanzhou 730000, China
| | - Xiaoli Yan
- School of Earth Sciences and Key Laboratory of Mineral Resources in Western China (Gansu Province), Lanzhou University, Lanzhou 730000, China
| | - Zhuo Zheng
- Guangdong Provincial Key Laboratory of Geodynamics and Geohazards, School of Earth Sciences and Engineering, Sun Yat-sen University, Zhuhai 519082, China
| | - Chunhui Song
- School of Earth Sciences and Key Laboratory of Mineral Resources in Western China (Gansu Province), Lanzhou University, Lanzhou 730000, China
| | - Torsten Utescher
- Senckenberg Research Institute, Frankfurt am Main, Steinmann Institute, Bonn University, 53115 Bonn, Germany
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16
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Judd EJ, Tierney JE, Huber BT, Wing SL, Lunt DJ, Ford HL, Inglis GN, McClymont EL, O'Brien CL, Rattanasriampaipong R, Si W, Staitis ML, Thirumalai K, Anagnostou E, Cramwinckel MJ, Dawson RR, Evans D, Gray WR, Grossman EL, Henehan MJ, Hupp BN, MacLeod KG, O'Connor LK, Sánchez Montes ML, Song H, Zhang YG. The PhanSST global database of Phanerozoic sea surface temperature proxy data. Sci Data 2022; 9:753. [PMID: 36473868 PMCID: PMC9726822 DOI: 10.1038/s41597-022-01826-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Paleotemperature proxy data form the cornerstone of paleoclimate research and are integral to understanding the evolution of the Earth system across the Phanerozoic Eon. Here, we present PhanSST, a database containing over 150,000 data points from five proxy systems that can be used to estimate past sea surface temperature. The geochemical data have a near-global spatial distribution and temporally span most of the Phanerozoic. Each proxy value is associated with consistent and queryable metadata fields, including information about the location, age, and taxonomy of the organism from which the data derive. To promote transparency and reproducibility, we include all available published data, regardless of interpreted preservation state or vital effects. However, we also provide expert-assigned diagenetic assessments, ecological and environmental flags, and other proxy-specific fields, which facilitate informed and responsible reuse of the database. The data are quality control checked and the foraminiferal taxonomy has been updated. PhanSST will serve as a valuable resource to the paleoclimate community and has myriad applications, including evolutionary, geochemical, diagenetic, and proxy calibration studies.
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Affiliation(s)
- Emily J Judd
- Smithsonian National Museum of Natural History, Department of Paleobiology, Washington, DC, 20560, USA.
| | - Jessica E Tierney
- University of Arizona, Department of Geosciences, Tuscon, AZ, 85721, USA
| | - Brian T Huber
- Smithsonian National Museum of Natural History, Department of Paleobiology, Washington, DC, 20560, USA
| | - Scott L Wing
- Smithsonian National Museum of Natural History, Department of Paleobiology, Washington, DC, 20560, USA
| | - Daniel J Lunt
- University of Bristol, School of Geographical Sciences, Bristol, BS8 1SS, UK
| | - Heather L Ford
- Queen Mary University of London, School of Geography, London, E1 4NS, UK
| | - Gordon N Inglis
- University of Southampton, School of Ocean and Earth Science, National Oceanography Centre Southampton, Southampton, SO14 3ZH, UK
| | | | | | | | - Weimin Si
- Brown University, Department of Earth, Environmental and Planetary Sciences, Providence, RI, 02912, USA
| | - Matthew L Staitis
- University of Edinburgh, School of Geosciences, Edinburgh, EH8 9XP, UK
| | | | - Eleni Anagnostou
- GEOMAR Helmholtz Centre for Ocean Research Kiel, 24148, Kiel, Germany
| | - Marlow Julius Cramwinckel
- University of Southampton, School of Ocean and Earth Science, National Oceanography Centre Southampton, Southampton, SO14 3ZH, UK
- Utrecht University, Department of Earth Sciences, Utrecht, 3584 CB, The Netherlands
| | - Robin R Dawson
- University of Massachusetts Amherst, Department of Geosciences, Amherst, MA, 01003, USA
| | - David Evans
- Goethe University Frankfurt, Institute of Geosciences, 60438, Frankfurt am Main, Germany
| | - William R Gray
- Université Paris-Saclay, Laboratoire des Sciences du Climat et de l'Environnement, Gif-sur-Yvette, France
| | - Ethan L Grossman
- Texas A&M University, Department of Geology and Geophysics, College Station, TX, 77843, USA
| | - Michael J Henehan
- GFZ German Research Centre for Geosciences, Section 3.3 Earth Surface Geochemistry, 14473, Potsdam, Germany
| | - Brittany N Hupp
- Oregon State University, College of Earth, Ocean and Atmospheric Sciences, Corvallis, OR, 97331, USA
| | - Kenneth G MacLeod
- University of Missouri, Department of Geological Sciences, Columbia, MO, 65211, USA
| | - Lauren K O'Connor
- University of Manchester, Department of Earth and Environmental Sciences, Manchester, M13 9PL, UK
| | | | - Haijun Song
- China University of Geosciences, State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, Wuhan, 430074, China
| | - Yi Ge Zhang
- Texas A&M University, Department of Oceanography, College Station, TX, 77843, USA
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17
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Yang LE, Sun L, Peng DL, Chen GJ, Sun H, Nie ZL. The significance of recent diversification in the Northern Hemisphere in shaping the modern global flora revealed from the herbaceous tribe of Rubieae (Rubiaceae). Mol Phylogenet Evol 2022; 177:107628. [PMID: 36096462 DOI: 10.1016/j.ympev.2022.107628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022]
Abstract
The global herbaceous flora is probably shaped by both ancient and/or recent diversification, companied with the impacts from geographic differences between the Northern and Southern Hemispheres. Therefore, its biogeographic pattern with respect to temporal and spatial divergence is far from full understanding. Tribe Rubieae, the largest herbaceous tribe in the woody-dominant Rubiaceae, provides an excellent opportunity for studying the macroevolution of worldwide colonization. Here, we aim to reconstruct the evolutionary history of Rubieae with regard to climate fluctuation and geological history in the Cenozoic. A total of 204 samples of Rubieae representing all the distribution areas of the tribe were used to infer its phylogenetic and biogeographic histories based on two nrDNA and six cpDNA regions. The ancestral area of Rubieae was reconstructed using a time-calibrated phylogeny in RASP and diversification rates were inferred using Bayesian analysis of macroevolutionary mixtures (BAMM). Our results show Rubieae probably originated in European region during the middle Oligocene, with the two subtribes separating at 26.8 million years ago (Ma). All the genera in Rubieae formed separate clades between 24.79 and 6.23 Ma. The ancestral area of the subtribe Rubiinae was the Madrean-Tethyan plant belt and the North Atlantic land bridge (NALB) provided passage between North America and Europe for Rubiinae. The subtribe Galiinae clade originated in Europe/central Asia during the late Oligocene. Two diversification shifts were detected within Rubieae in the late Neogene. Most extant Rubieae species diverged recently during the Neogene within clades that generally were established during the late Paleogene. The tribe shows complex migration/dispersal patterns within the North Hemisphere combined with multiple recent dispersals into Southern Hemisphere. Our results highlighted the important role of recent biogeographic diversification in the Northern Hemisphere in shaping the modern global herbaceous flora during the latest and rapid worldwide expansion in the Neogene.
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Affiliation(s)
- Li-E Yang
- Key Laboratory for Plant Diversity and Biogeography of Eastern Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China; Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Change, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
| | - Lu Sun
- Key Laboratory for Plant Diversity and Biogeography of Eastern Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Li Peng
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Guang-Jie Chen
- Yunnan Key Laboratory of Plateau Geographical Processes and Environmental Change, Faculty of Geography, Yunnan Normal University, Kunming 650500, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of Eastern Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China.
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18
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Luo Y, Li S. The stepwise Indian-Eurasian collision and uplift of the Himalayan-Tibetan plateau drove the diversification of high-elevation Scytodes spiders. Cladistics 2022; 38:582-594. [PMID: 35802675 DOI: 10.1111/cla.12512] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 01/31/2023] Open
Abstract
The Cenozoic Indian-Eurasian collision and uplift of the Himalayan-Tibetan Plateau (HTP) are among the most important geological events in the world. They have affected the diversification of regional biota of many taxonomic groups on and around the HTP. However, the exact timing and model of the collision and uplift events and speciation on and around the HTP are still in debate. The Himalayas group of Scytodes spitting spiders (Araneae: Scytodidae) are distributed at high elevations of the HTP and northern Indochina. Here, we reconstruct a dated molecular phylogeny for pan-Himalayan Scytodes spiders, including the Himalayas group, with full geographical sampling of the species from the HTP and Indochina. We test a hypothesis to explain that the rich montane biodiversity of the region is uplift-driven diversification-that orogeny drives rapid in situ speciation of the resident Scytodes lineages. Our findings revealed that the separation of the Himalayas clade from the Myanmar clade took place during the middle Oligocene, reflecting the final collision of India with Eurasia. The deep divergences among three clades (the Himalayas, the Myanmar and the Indochina clades) occurred from the middle Eocene to the middle Oligocene, corresponding to two early uplift events of the HTP. The evolutionary split between the Himalayas + Myanmar and Indochina clades were simultaneous with the rapid lateral extrusion of Indochina by the initial Himalayan uplift around the Eocene. This study highlights the importance of the diversification of dispersal-limited, high-elevation invertebrates as independent lines of evidence to reflect key tectonic events in the Himalayan-Indochina region, supporting the stepwise model for the Indian-Eurasian collision and uplift of HTP.
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Affiliation(s)
- Yufa Luo
- School of Life Sciences, Shaoxing University, Shaoxing, 312000, China.,School of Life Sciences, Gannan Normal University, Ganzhou, 341000, China.,School of Life Sciences, Shangrao Normal University, Shangrao, 334001, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
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19
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Huang YX, Xing ZP, Zhang H, Xu ZB, Tao LL, Hu HY, Kitching IJ, Wang X. Characterization of the Complete Mitochondrial Genome of Eight Diurnal Hawkmoths (Lepidoptera: Sphingidae): New Insights into the Origin and Evolution of Diurnalism in Sphingids. INSECTS 2022; 13:887. [PMID: 36292835 PMCID: PMC9604448 DOI: 10.3390/insects13100887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
In this study, the mitochondrial genomes of 22 species from three subfamilies in the Sphingidae were sequenced, assembled, and annotated. Eight diurnal hawkmoths were included, of which six were newly sequenced (Hemaris radians, Macroglossum bombylans, M. fritzei, M. pyrrhosticta, Neogurelca himachala, and Sataspes xylocoparis) and two were previously published (Cephonodes hylas and Macroglossum stellatarum). The mitochondrial genomes of these eight diurnal hawkmoths were comparatively analyzed in terms of sequence length, nucleotide composition, relative synonymous codon usage, non-synonymous/synonymous substitution ratio, gene spacing, and repeat sequences. The mitogenomes of the eight species, ranging in length from 15,201 to 15,461 bp, encode the complete set of 37 genes usually found in animal mitogenomes. The base composition of the mitochondrial genomes showed A+T bias. The most commonly used codons were UUA (Leu), AUU (Ile), UUU (Phe), AUA (Met), and AAU (Asn), whereas GCG (Ala) and CCG (Pro) were rarely used. A phylogenetic tree of Sphingidae was constructed based on both maximum likelihood and Bayesian methods. We verified the monophyly of the four current subfamilies of Sphingidae, all of which had high support. In addition, we performed divergence time estimation and ancestral character reconstruction analyses. Diurnal behavior in hawkmoths originated 29.19 million years ago (Mya). It may have been influenced by the combination of herbaceous flourishing, which occurred 26-28 Mya, the uplift of the Tibetan Plateau, and the large-scale evolution of bats in the Oligocene to Pre-Miocene. Moreover, diurnalism in hawkmoths had multiple independent origins in Sphingidae.
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Affiliation(s)
- Yi-Xin Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Zhi-Ping Xing
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Hao Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Zhen-Bang Xu
- Institute of Resource Plants, Yunnan University, Kunming 650500, China
| | - Li-Long Tao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Hao-Yuan Hu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | | | - Xu Wang
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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20
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Yisilam G, Wang CX, Xia MQ, Comes HP, Li P, Li J, Tian XM. Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:915526. [PMID: 35845630 PMCID: PMC9280156 DOI: 10.3389/fpls.2022.915526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure and the phylogeographic history of Lycium ruthenicum, a plant species adapted to the climate in northwestern China. We identified 20 chloroplast haplotypes of which two were dominant and widely distributed in almost all populations. The species has high haplotype diversity and low nucleotide diversity based on the cpDNA data. The EST-SSR results showed a high percentage of total genetic variation within populations. Both the cpDNA and EST-SSR results indicated no significant differentiation among populations. By combining the evidence from ENM and demographic analysis, we confirmed that both the last interglacial (LIG) and late-glacial maximum (LGM) climatic fluctuations, aridification might have substantially narrowed the distribution range of this desert species, the southern parts of the Junggar Basin, the Tarim Basin, and the eastern Pamir Plateau were the potential glacial refugia for L. ruthenicum during the late middle Pleistocene to late Pleistocene Period. During the early Holocene, the warm, and humid climate promoted its demographic expansion in northwestern China. This work may provide new insights into the mechanism of formation of plant diversity in this arid region.
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Affiliation(s)
- Gulbar Yisilam
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen-Xi Wang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Mao-Qin Xia
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hans Peter Comes
- Department of Environment and Biodiversity, University of Salzburg, Salzburg, Austria
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jin Li
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Xin-Min Tian
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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21
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Yuan L, Chen S, Wang Y, Ma Y. The molecular characteristics of gastric cancer patients living in Qinghai-Tibetan Plateau. BMC Gastroenterol 2022; 22:244. [PMID: 35568828 PMCID: PMC9107197 DOI: 10.1186/s12876-022-02324-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Gastric cancer, or stomach cancer, that originates in the inner lining of the stomach, was the fifth most common cancer and the fourth mortality globally, with over one million new cases in 2020 and an estimated 769,000 deaths. The molecular characteristics of gastric cancer has been complicated by histological and intratumor heterogeneity. The incidence of gastric cancer shows wide geographical variation. As the largest and highest region in China, Qinghai-Tibetan Plateau is one of the important global biodiversity hotspots. Here, we collect tumour and paired normal bio-samples from 31 primary gastric cancer patients from Qinghai Provincial People's Hospital, and discuss the molecular characteristics for gastric cancer patients living in plateau. They have more single nucleotide polymorphisms (SNP) located in chromosome 7 with C → T and G → A as the most common alteration types, barely share the cancer driver genes with western patients, and have no significant differences in various Chinese nation. These characteristics offers a great opportunity to further understanding the divergent mechanism of gastric cancer, increase the efficacy for diagnosis and prognosis, finally lead the optimal targeted therapeutics.
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Affiliation(s)
- Ling Yuan
- Medical College, Soochow University, Suzhou, 215123, Jiangsu, China.,Department of Gastroenterology, Qinghai Provincial People's Hospital, Xining, 810007, Qinghai, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.,Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, 810008, China
| | - Yongcui Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China. .,Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Yingcai Ma
- Department of Gastroenterology, Qinghai Provincial People's Hospital, Xining, 810007, Qinghai, China.
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22
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Yang Z, Ma W, He X, Zhao T, Yang X, Wang L, Ma Q, Liang L, Wang G. Species divergence and phylogeography of Corylus heterophylla Fisch complex (Betulaceae): Inferred from molecular, climatic and morphological data. Mol Phylogenet Evol 2022; 168:107413. [PMID: 35031460 DOI: 10.1016/j.ympev.2022.107413] [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: 06/22/2021] [Revised: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 10/19/2022]
Abstract
Historical geo-climatic changes have shaped the geographical distributions and genetic diversity of numerous plant taxa in East Asia, which promote species divergence and ultimately speciation. Here, we integrated multiple approaches, including molecular phylogeography, ecological niche modeling, and morphological traits to examine the nucleotide diversity and interspecific divergence within Corylus heterophylla complex (C. heterophylla, C. kweichowensis, and C. yunnanensis). These three sibling taxa harbored similar high levels of nucleotide diversity at the species level. The molecular data (SCNG and cpDNA) unanimously supported the division of C. heterophylla complex into two major clades, with C. yunnanensis diverged earlier from the complex, whereas C. heterophylla and C. kweichowensis could hardly be separated. The split between the two clades (c. 12.89 Ma) coincided with the formation of Sichuan Basin in the middle Miocene, while the divergence among and within the five subclades (YUN1-YUN3, HK1-HK2) occurred from the late Miocene to the Pleistocene. C. heterophylla of northern China experienced glacial contraction and interglacial expansion during the Quaternary, whereas C. kweichowensis and C. yunnanensis of southern China presented population expansion even during the last glacial maximum. Despite of high levels of genetic admixture between C. heterophylla and C. kweichowensis, significant ecological and morphological discrepancy as well as incomplete geographic isolation indicated that adaptive evolution triggered by divergent selection may have played important roles in incipient ecological speciation.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Xin He
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
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23
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Du WB, Jia P, Du GZ. Current patterns of plant diversity and phylogenetic structure on the Kunlun Mountains. PLANT DIVERSITY 2022; 44:30-38. [PMID: 35281127 PMCID: PMC8897310 DOI: 10.1016/j.pld.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 06/14/2023]
Abstract
Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology. The Qinghai-Tibet Plateau serves as a natural laboratory for studying these issues. However, most previous studies have focused on the entire Qinghai-Tibet Plateau, leaving independent physical geographic subunits in the region less well understood. We studied the current plant diversity of the Kunlun Mountains, an independent physical geographic subunit located in northwestern China on the northern edge of the Qinghai-Tibet Plateau. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, phylogenetic diversity, and community phylogenetic structure of the current plant diversity in the area. The distribution patterns of 1911 seed plants showed that species were distributed mainly in the eastern regions of the Kunlun Mountains. The taxonomic richness, phylogenetic diversity, and genera richness showed that the eastern regions of the Kunlun Mountains should be the priority area of biodiversity conservation, particularly the southeastern regions. The proportion of Chinese endemic species inhabiting the Kunlun Mountains and their floristic similarity may indicate that the current patterns of species diversity were favored via species colonization. The Hengduan Mountains, a biodiversity hotspot, is likely the largest source of species colonization of the Kunlun Mountains after the Quaternary. The net relatedness index indicated that 20 of the 28 communities examined were phylogenetically dispersed, while the remaining communities were phylogenetically clustered. The nearest taxon index indicated that 27 of the 28 communities were phylogenetically clustered. These results suggest that species colonization and habitat filtering may have contributed to the current plant diversity of the Kunlun Mountains via ecological and evolutionary processes, and habitat filtering may play an important role in this ecological process.
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24
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Zhang G, Han Y, Wang H, Wang Z, Xiao H, Sun M. Phylogeography of Iris loczyi (Iridaceae) in Qinghai-Tibet Plateau revealed by chloroplast DNA and microsatellite markers. AOB PLANTS 2021; 13:plab070. [PMID: 34876969 PMCID: PMC8643446 DOI: 10.1093/aobpla/plab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Quaternary climate oscillations and complex topography have tremendous effects on current distribution and genetic structure of species, and hence the Qinghai-Tibet Plateau (QTP), the largest plateau in the world, has become a hotspot for many phylogeographic studies. However, little is known about the phylogeographic pattern of herbaceous plants in QTP. Here, we investigate the genetic diversity, population structure and historical dynamics of Iris loczyi, using five chloroplast DNA (cpDNA) fragments and seven microsatellite markers. A total of 15 populations, and 149 individuals were sampled throughout the QTP. High genetic diversity was detected both in cpDNA (H d = 0.820) and SSR (H o = 0.689, H e = 0.699). Ten cpDNA haplotypes and 163 alleles were identified. AMOVA and clustering analyses revealed obvious differentiation between regions. The N st, G st and Mantel test showed significant phylogeographic structure of I. loczyi. The neutrality test and mismatch distribution analyses indicated that I. loczyi could not have undergone a historical population expansion, but population XS from the Qilian Mountain area could have experienced a local expansion. Bottleneck analyses indicated that I. loczyi had not experienced bottleneck recently. Based on cpDNA and SSR results, the Qilian Mountain area was inferred as a potential glacial refuge, and the southern Tibet valley was considered as a 'microrefugia' for I. loczyi. These findings provided new insights into the location of glacial refuges for the species distributed in QTP, and supplemented more plant species data for the response of QTP species to the Quaternary climate.
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Affiliation(s)
- Guoli Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Yan Han
- Qian’an No. 1 Middle School, Tangshan 063000, China
| | - Huan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Ziyang Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Mingzhou Sun
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun 130024, China
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25
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Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers. FORESTS 2021. [DOI: 10.3390/f12091164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.
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26
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Denk T, Bouchal JM. New Fagaceous pollen taxa from the Miocene Søby flora of Denmark and their biogeographic implications. AMERICAN JOURNAL OF BOTANY 2021; 108:1500-1524. [PMID: 34458984 DOI: 10.1002/ajb2.1716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The Fagaceae comprise around 1000 tree species in the Northern Hemisphere. Despite an extensive fossil pollen record, reconstructing biogeographic patterns is hampered because it is difficult to achieve good taxonomic resolution with light microscopy alone. We investigate dispersed pollen of Fagaceae from the Miocene Søby flora, Denmark. We explore the latitudinal gradient in Fagaceae distribution during the Miocene Climatic Optimum (MCO) in Europe and the Northern Hemisphere to compare it with the Eocene Warmhouse and the present. METHODS We investigated dispersed pollen using light and scanning electron microscopy. We assessed biogeographic patterns in Fagaceae during two warm periods in Earth history (MCO, Eocene) and the present. RESULTS Eight species of Fagaceae were recognized in the Søby flora. Of these, Fagus had a continuous Mediterranean to subarctic distribution during MCO; Quercus sect. Cerris and castaneoids had northern limits in Denmark, and evergreen Quercus sect. Ilex in Central Europe. In a northern hemispheric context, Fagus and sections of Quercus had more northerly distribution limits during Eocene and MCO with maximum northward extensions during Eocene (Fagus, castaneoids) or Oligo-Miocene (Quercus sects. Cerris and Ilex). The known distribution of the extinct Tricolporopollenites theacoides during MCO included Central Europe and East China, while this taxon thrived in South China during Eocene. CONCLUSIONS More northerly distributions during MCO and Eocene probably were determined by temperature. In contrast, fossil occurrences in areas that are arid or semi-humid today were determined by maritime conditions in these areas (western North America, Central Asia) during the Cenozoic.
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Affiliation(s)
- Thomas Denk
- Department of Paleobiology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Johannes M Bouchal
- Aerobiology and Pollen Information, Medical University of Vienna, Vienna, Austria
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Yang B, Li L, Liu J, Zhang L. Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau. PLANT DIVERSITY 2021; 43:198-205. [PMID: 34195504 PMCID: PMC8233517 DOI: 10.1016/j.pld.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 05/09/2023]
Abstract
The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum (Fagopyrum) tibeticum. Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum (Fagopyrum) tibeticum, Atraphaxis bracteata and Calligonum ebinuricum. Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum (Fagopyrum) tibeticum, A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum. Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum, which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.
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28
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Ye H, Wang Z, Hou H, Wu J, Gao Y, Han W, Ru W, Sun G, Wang Y. Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species. BMC Ecol Evol 2021; 21:56. [PMID: 33858342 PMCID: PMC8050911 DOI: 10.1186/s12862-021-01790-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/08/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Climate heterogeneity not only indirectly shapes the genetic structures of plant populations, but also drives adaptive divergence by impacting demographic dynamics. The variable localized climates and topographic complexity of the Taihang Mountains make them a major natural boundary in Northern China that influences the divergence of organisms distributed across this region. Opisthopappus is an endemic genus of the Taihang Mountains that includes only two spatially partitioned species Opisthopappus longilobus and Opisthopappus taihangensis. For this study, the mechanisms behind the genetic variations in Opisthopappus populations were investigated. RESULTS Using SNP and InDel data coupled with geographic and climatic information, significant genetic differentiation was found to exist either between Opisthopappus populations or two species. All studied populations were divided into two genetic groups with the differentiation of haplotypes between the groups. At approximately 17.44 Ma of the early Miocene, O. taihangensis differentiated from O. longilobus under differing precipitation regimes due to the intensification of the Asian monsoon. Subsequently, intraspecific divergence might be induced by the dramatic climatic transformation from the mid- to late Miocene. During the Pleistocene period, the rapid uplift of the Taihang Mountains coupled with violent climatic oscillations would further promote the diversity of the two species. Following the development of the Taihang Mountains, its complex topography created geographical and ecological heterogeneity, which could lead to spatiotemporal isolation between the Opisthopappus populations. Thus the adaptive divergence might occur within these intraspecific populations in the localized heterogeneous environment of the Taihang Mountains. CONCLUSIONS The localized environmental events through the integration of small-scale spatial effects impacted the demographic history and differentiation mechanism of Opisthopappus species in the Taihang Mountains. The results provide useful information for us to understand the ecology and evolution of organisms in the mountainous environment from population and species perspective.
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Affiliation(s)
- Hang Ye
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Huimin Hou
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Jiahui Wu
- College of Life Science, Shanxi Normal University, Linfen, China
- Changzhi University, Changzhi, China
| | - Yue Gao
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Wei Han
- College of Life Science, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Saint Mary's University, Halifax, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, China.
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29
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Meng R, Meng Y, Yang YP, Nie ZL. Phylogeny and biogeography of Maianthemum (Asparagaceae: Nolinoideae) revisited with emphasis on its divergence pattern in SW China. PLANT DIVERSITY 2021; 43:93-101. [PMID: 33997541 PMCID: PMC8103418 DOI: 10.1016/j.pld.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 05/30/2023]
Abstract
Maianthemum is a genus with more than 35 species from the tribe Polygonateae (Asparagaceae), widely distributed between North to Central Americas and eastern Asia with high diversity in the eastern Himalayas to the Hengduan Mountains of SW China. Although most species from SW China form a well-supported clade, phylogenetic relationships within this clade remain unclear. With a broad level of taxon sampling and an extensive character sampling from eight DNA regions, this study intends to revisit the phylogeny and biogeography of the genus to better understand the divergence patterns of species from SW China. Phylogenetic results suggested the monophyly of Maianthemum with recognition of nine strongly supported clades, but backbone relationships among these clades remained largely uncertain. For the SW China clade, individuals from the same species are grouped into different lineages. Our results revealed that the fast radiation of the SW China clade was occurred in the eastern Himalayas, followed by subsequent radiation in the Hengduan Mountains in the Pliocene. Intercontinental disjunctions of Maianthemum in the Northern Hemisphere appear to have occurred multiple times during the late Miocene to the Pliocene, likely resulted by a combination of both vicariance and long-distance dispersal events.
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Affiliation(s)
- Ran Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China
| | - Ying Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China
| | - Yong-Ping Yang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou 416000, Hunan, China
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30
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Rana SK, Luo D, Rana HK, Chen S, Sun H. Molecular phylogeny, biogeography and character evolution of the montane genus Incarvillea Juss. (Bignoniaceae). PLANT DIVERSITY 2021; 43:1-14. [PMID: 33778220 PMCID: PMC7987631 DOI: 10.1016/j.pld.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 06/01/2023]
Abstract
The complex orogeny of the Himalaya and the Qinghai-Tibet Plateau (QTP) fosters habitat fragmentation that drives morphological differentiation of mountain plant species. Consequently, determining phylogenetic relationships between plant subgenera using morphological characters is unreliable. Therefore, we used both molecular phylogeny and historical biogeographic analysis to infer the ancestral states of several vegetative and reproductive characters of the montane genus Incarvillea. We determined the taxonomic position of the genus Incarvillea within its family and inferred the biogeographical origin of taxa through Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) analyses using three molecular data sets (trnL-trnF sequences, nr ITS sequences, and a data set of combined sequences) derived from 81% of the total species of the genus Incarvillea. Within the genus-level phylogenetic framework, we examined the character evolution of 10 key morphological characters, and inferred the ancestral area and biogeographical history of the genus. Our analyses revealed that the genus Incarvillea is monophyletic and originated in Central Asia during mid-Oligocene ca. 29.42 Ma. The earliest diverging lineages were subsequently split into the Western Himalaya and Sino-Himalaya during the early Miocene ca. 21.12 Ma. These lineages resulted in five re-circumscribed subgenera (Amphicome, Olgaea, Niedzwedzkia, Incarvillea, and Pteroscleris). Moreover, character mapping revealed the ancestral character states of the genus Incarvillea (e.g., suffruticose habit, cylindrical capsule shape, subligneous capsule texture, absence of capsule wing, and loculicidal capsule dehiscence) that are retained at the earliest diverging ancestral nodes across the genus. Our phylogenetic tree of the genus Incarvillea differs from previously proposed phylogenies, thereby recommending the placement of the subgenus Niedzwedzkia close to the subgenus Incarvillea and maintaining two main divergent lineages.
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Affiliation(s)
- Santosh Kumar Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dong Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hum Kala Rana
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shaotian Chen
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Hang Sun
- 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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31
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Spicer RA, Su T, Valdes PJ, Farnsworth A, Wu FX, Shi G, Spicer TEV, Zhou Z. Why 'the uplift of the Tibetan Plateau' is a myth. Natl Sci Rev 2021; 8:nwaa091. [PMID: 34691550 PMCID: PMC8288424 DOI: 10.1093/nsr/nwaa091] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
The often-used phrase 'the uplift of the Tibetan Plateau' implies a flat-surfaced Tibet rose as a coherent entity, and that uplift was driven entirely by the collision and northward movement of India. Here, we argue that these are misconceptions derived in large part from simplistic geodynamic and climate modeling, as well as proxy misinterpretation. The growth of Tibet was a complex process involving mostly Mesozoic collisions of several Gondwanan terranes with Asia, thickening the crust and generating complex relief before the arrival of India. In this review, Earth system modeling, paleoaltimetry proxies and fossil finds contribute to a new synthetic view of the topographic evolution of Tibet. A notable feature overlooked in previous models of plateau formation was the persistence through much of the Cenozoic of a wide east-west orientated deep central valley, and the formation of a plateau occurred only in the late Neogene through compression and internal sedimentation.
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Affiliation(s)
- Robert A Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes MK7 6AA, UK
| | - Tao Su
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Paul J Valdes
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
| | | | - Fei-Xiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Gongle Shi
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Teresa E V Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Zhekun Zhou
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
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32
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Wang YL, Lu JM, Zhang Y, Chen HW. Molecular phylogeny, species delimitation and biogeographic history of the Stegana (Steganina) shirozui species group (Diptera: Drosophilidae) from East Asia. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Stegana (Steganina) shirozui species group is mainly distributed in East Asia. In the present study, the molecular phylogeny of the S. shirozui group was investigated based on mitochondrial (COI and ND2) and nuclear (28S rRNA) markers. The resulting trees support the S. shirozui group as monophyletic and indicate that in this group, species associated with closer affinities show higher structural homogeneity in male genitalia. Molecular species delimitation assess most species limits and recognize four new species in the S. shirozui group from south-west China: S. alianya sp. nov., S. diodonta sp. nov., S. zebromyia sp. nov. and S. zopheria sp. nov. One new synonym was also recognized. Additionally, three typical male genital characters of the S. shirozui group were placed on the molecular phylogenetic framework. The outcome of both divergence-time estimation and ancestral area reconstruction suggests that the S. shirozui group likely originated in south-west China in the Middle Miocene.
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Affiliation(s)
- Ya-Lian Wang
- Department of Entomology, South China Agricultural University, Tianhe, Guangzhou, China
| | - Jin-Ming Lu
- Department of Entomology, South China Agricultural University, Tianhe, Guangzhou, China
| | - Yuan Zhang
- Department of Entomology, South China Agricultural University, Tianhe, Guangzhou, China
| | - Hong-Wei Chen
- Department of Entomology, South China Agricultural University, Tianhe, Guangzhou, China
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33
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The evolutionary origin and domestication history of goldfish ( Carassius auratus). Proc Natl Acad Sci U S A 2020; 117:29775-29785. [PMID: 33139555 DOI: 10.1073/pnas.2005545117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish-the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.
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34
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Ding WN, Ree RH, Spicer RA, Xing YW. Ancient orogenic and monsoon-driven assembly of the world's richest temperate alpine flora. Science 2020; 369:578-581. [PMID: 32732426 DOI: 10.1126/science.abb4484] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/08/2020] [Indexed: 12/25/2022]
Abstract
Understanding how alpine biotas formed in response to historical environmental change may improve our ability to predict and mitigate the threats to alpine species posed by global warming. In the world's richest temperate alpine flora, that of the Tibet-Himalaya-Hengduan region, phylogenetic reconstructions of biome and geographic range evolution show that extant lineages emerged by the early Oligocene and diversified first in the Hengduan Mountains. By the early to middle Miocene, accelerated diversification and colonization of adjacent regions were likely driven jointly by mountain building and intensification of the Asian monsoon. The alpine flora of the Hengduan Mountains has continuously existed far longer than any other alpine flora on Earth and illustrates how modern biotas have been shaped by past geological and climatic events.
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Affiliation(s)
- Wen-Na Ding
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Richard H Ree
- Negaunee Integrative Research Center, Field Museum, Chicago, IL 60605, USA.
| | - Robert A Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China.,School of Environment, Earth, and Ecosystem Sciences, The Open University, Milton Keynes MK7 6AA, UK
| | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China. .,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
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35
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Spicer RA, Farnsworth A, Su T. Cenozoic topography, monsoons and biodiversity conservation within the Tibetan Region: An evolving story. PLANT DIVERSITY 2020; 42:229-254. [PMID: 33094197 PMCID: PMC7567768 DOI: 10.1016/j.pld.2020.06.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 05/06/2023]
Abstract
The biodiversity of the Himalaya, Hengduan Mountains and Tibet, here collectively termed the Tibetan Region, is exceptional in a global context. To contextualize and understand the origins of this biotic richness, and its conservation value, we examine recent fossil finds and review progress in understanding the orogeny of the Tibetan Region. We examine the deep-time origins of monsoons affecting Asia, climate variation over different timescales, and the establishment of environmental niche heterogeneity linked to topographic development. The origins of the modern biodiversity were established in the Eocene, concurrent with the formation of pronounced topographic relief across the Tibetan Region. High (>4 km) mountains to the north and south of what is now the Tibetan Plateau bounded a Paleogene central lowland (<2.5 km) hosting moist subtropical vegetation influenced by an intensifying monsoon. In mid Miocene times, before the Himalaya reached their current elevation, sediment infilling and compressional tectonics raised the floor of the central valley to above 3000 m, but central Tibet was still moist enough, and low enough, to host a warm temperate angiosperm-dominated woodland. After 15 Ma, global cooling, the further rise of central Tibet, and the rain shadow cast by the growing Himalaya, progressively led to more open, herb-rich vegetation as the modern high plateau formed with its cool, dry climate. In the moist monsoonal Hengduan Mountains, high and spatially extensive since the Eocene but subsequently deeply dissected by river incision, Neogene cooling depressed the tree line, compressed altitudinal zonation, and created strong environmental heterogeneity. This served as a cradle for the then newly-evolving alpine biota and favoured diversity within more thermophilic vegetation at lower elevations. This diversity has survived through a combination of minimal Quaternary glaciation, and complex relief-related environmental niche heterogeneity. The great antiquity and diversity of the Tibetan Region biota argues for its conservation, and the importance of that biota is demonstrated through our insights into its long temporal gestation provided by fossil archives and information written in surviving genomes. These data sources are worthy of conservation in their own right, but for the living biotic inventory we need to ask what it is we want to conserve. Is it 1) individual taxa for their intrinsic properties, 2) their services in functioning ecosystems, or 3) their capacity to generate future new biodiversity? If 2 or 3 are our goal then landscape conservation at scale is required, and not just seed banks or botanical/zoological gardens.
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Affiliation(s)
- Robert A. Spicer
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
- School of Environmental, Earth and Ecosystem Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | | | - Tao Su
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
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36
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Rong G, Zhang Y, Ma Y, Chen S, Wang Y. The Clinical and Molecular Characterization of Gastric Cancer Patients in Qinghai-Tibetan Plateau. Front Oncol 2020; 10:1033. [PMID: 32695679 PMCID: PMC7339979 DOI: 10.3389/fonc.2020.01033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Gastric cancer was the fifth most common malignancy and the third deadliest cancer (738,000 deaths in 2018) in the world. The analysis of its molecular characteristics has been complicated by histological and intratumor heterogeneity. Furthermore, the previous studies indicate that the incidence of gastric cancer shows wide geographical variation. As the largest and highest region in China, Qinghai-Tibetan Plateau (QTP) is one of the important global biodiversity hotspots. Here, to better understand the mechanism of gastric cancer and offer the targeted therapeutic strategies specially designed for patients in QTP, we collect tumor and blood samples from 30 primary gastric adenocarcinoma cancer patients at Qinghai Provincial People's Hospital. We discuss the clinical and molecular characteristics for these patients that have been ascribed to the unique features in this place, including high altitude (the average height above sea level is around 4,000 m), multi-ethnic groups, and the specific ways of life or habits (such as eating too much beef and mutton, have alcohol and cigarette problem, et al.). By comparing with the western gastric cancer patients collected from TCGA data portal, some unique characteristics for patients in QTP are suggested. They include high incidence in younger people, most of tumor are located in body, most of SNP are detected in chromosome 7, and the very different molecular atlas in minor ethnic groups and Han Chinese. These characteristics will provide the unprecedented opportunity to increase the efficacy for diagnosis and prognosis of gastric cancer in QTP. Furthermore, to suggest the targeted therapeutics specially designed for these 30 patients, an adapted kernel-based learning model and a compilation of pharmacogenomics data of 462 patient-derived tumor cells (PDCs) that illustrate the diverse genetic and molecular backgrounds of cancer patients, were introduced. In conclusion, our study offers a big opportunity to better understand the mechanism of gastric cancer in QTP and guide the optimal patient-tailored therapy for them.
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Affiliation(s)
- Guanghong Rong
- Department of Gastroenterology, Qinghai Provincial People's Hospital, Xining, China
| | - Yongxia Zhang
- Department of Gynecology, Qinghai Provincial People's Hospital, Xining, China
| | - Yingcai Ma
- Department of Gastroenterology, Qinghai Provincial People's Hospital, Xining, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
| | - Yongcui Wang
- Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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37
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Farnsworth A, Lunt DJ, Robinson SA, Valdes PJ, Roberts WHG, Clift PD, Markwick P, Su T, Wrobel N, Bragg F, Kelland SJ, Pancost RD. Past East Asian monsoon evolution controlled by paleogeography, not CO 2. SCIENCE ADVANCES 2019; 5:eaax1697. [PMID: 31692956 PMCID: PMC6821471 DOI: 10.1126/sciadv.aax1697] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/17/2019] [Indexed: 05/03/2023]
Abstract
The East Asian monsoon plays an integral role in human society, yet its geological history and controlling processes are poorly understood. Using a general circulation model and geological data, we explore the drivers controlling the evolution of the monsoon system over the past 150 million years. In contrast to previous work, we find that the monsoon is controlled primarily by changes in paleogeography, with little influence from atmospheric CO2. We associate increased precipitation since the Late Cretaceous with the gradual uplift of the Himalayan-Tibetan region, transitioning from an ITCZ-dominated monsoon to a sea breeze-dominated monsoon. The rising region acted as a mechanical barrier to cold and dry continental air advecting into the region, leading to increasing influence of moist air from the Indian Ocean/South China Sea. We show that, apart from a dry period in the middle Cretaceous, a monsoon system has existed in East Asia since at least the Early Cretaceous.
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Affiliation(s)
- Alex Farnsworth
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Cabot Institute, University of Bristol, Bristol BS8 1UJ, UK
- Corresponding author.
| | - Daniel J. Lunt
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Cabot Institute, University of Bristol, Bristol BS8 1UJ, UK
| | | | - Paul J. Valdes
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Cabot Institute, University of Bristol, Bristol BS8 1UJ, UK
| | - William H. G. Roberts
- Department of Geography and Environmental Science, Northumbria University, Newcastle upon Tyne, UK
| | - Peter D. Clift
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA
- Research Center for Earth System Science, Yunnan University, Chenggong District, Kunming, Yunnan 650091, PR China
| | | | - Tao Su
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | | | - Fran Bragg
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Cabot Institute, University of Bristol, Bristol BS8 1UJ, UK
| | | | - Richard D. Pancost
- Cabot Institute, University of Bristol, Bristol BS8 1UJ, UK
- Organic Geochemistry Unit, School of Earth Sciences, and School of Chemistry, University of Bristol, Bristol BS8 1RJ, UK
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38
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Xu LS, Herrando-Moraira S, Susanna A, Galbany-Casals M, Chen YS. Phylogeny, origin and dispersal of Saussurea (Asteraceae) based on chloroplast genome data. Mol Phylogenet Evol 2019; 141:106613. [PMID: 31525421 DOI: 10.1016/j.ympev.2019.106613] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022]
Abstract
Saussurea is one of the largest genera of the tribe Cardueae of Asteraceae, comprising about 460 species from the Northern Hemisphere with most species distributed in QTPss and adjacent areas. Here, we established a well-supported phylogenetic framework for Saussurea based on whole chloroplast genomes of 136 taxa plus 16 additional taxa of Cardueae using Bayesian inference and Maximum Likelihood. Our phylogenetic results are inconsistent with previous subgeneric classifications of Saussurea. We nearly completely delimited subgen. Eriocoryne, and found that subgen. Theodorea, subgen. Saussurea section Laguranthera and Rosulascentes are closely related to each other. Based on our phylogenetic results, we performed biogeographic analyses and inferred that the genus Saussurea arose during early-middle Miocene within the Hengduan Mountains. We expect that landscape heterogeneity within the QTPss and adjacent areas, such as the Hengduan Mountains, played an important role in the evolution of Saussurea. Following its evolutionary origin, the genus underwent rapid diversification in situs and dispersed northwards in several migrational patterns. Both continuous uplift of the QTPss and adjacent areas as well as global cooling since mid-Miocene probably led to geographic expansion and diffusion of Saussurea, with the latter, in particular, resulting in the northward dispersal.
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Affiliation(s)
- Lian-Sheng Xu
- 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
| | - Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, ES-08193 Bellaterra, Spain
| | - You-Sheng 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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Li Y, Zhu J, Ge C, Wang Y, Zhao Z, Ma S, Hoffmann AA, Endersby NM, Liu Q, Yu W, Jiang W. Molecular Phylogeny and Historical Biogeography of the Butterfly Tribe Aeromachini Tutt (Lepidoptera: Hesperiidae) from China. Cells 2019; 8:E294. [PMID: 30934977 PMCID: PMC6523876 DOI: 10.3390/cells8040294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/16/2022] Open
Abstract
: The butterfly tribe Aeromachini Tutt, 1906 is a large group of skippers. In this study, a total of 10 genera and 45 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2093 bp). The combined dataset was analyzed with maximum likelihood inference using IQtree. We found strong support for monophyly of Aeromachini from China and support for the most recent accepted species in the tribe. Two paraphyletic genera within Aeromachini are presented and discussed. The divergence time estimates with BEAST and ancestral-area reconstructions with RASP provide a detailed description about the historical biogeography of the Aeromachini from China. The tribe very likely originated from the Hengduan Mountains in the late Ecocene and expanded to the Himalaya Mountains and Central China Regions. A dispersal-vicariance analysis suggests that dispersal events have played essential roles in the distribution of extant species, and geological and climatic changes have been important factors driving current distribution patterns.
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Affiliation(s)
- Yuanyuan Li
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Jianqing Zhu
- Shanghai Zoological Park, Shanghai 200335, China.
| | - Chen Ge
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Ying Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Zimiao Zhao
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Shuojia Ma
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Ary A Hoffmann
- School of BioSciences, The University of Melbourne, Bio21 Institute, Parkville, Victoria 3052, Australia.
| | - Nancy M Endersby
- School of BioSciences, The University of Melbourne, Bio21 Institute, Parkville, Victoria 3052, Australia.
| | - Qunxiu Liu
- Shanghai Zoological Park, Shanghai 200335, China.
| | - Weidong Yu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Weibin Jiang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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Liang Y, Zhang Y, Wen J, Su X, Ren Z. Evolutionary History of Rhus chinensis (Anacardiaceae) From the Temperate and Subtropical Zones of China Based on cpDNA and Nuclear DNA Sequences and Ecological Niche Model. Front Genet 2019; 10:171. [PMID: 30891066 PMCID: PMC6411847 DOI: 10.3389/fgene.2019.00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 02/15/2019] [Indexed: 11/28/2022] Open
Abstract
To explore the origin and evolution of local flora and vegetation, we examined the evolutionary history of Rhus chinensis, which is widely distributed in China’s temperate and subtropical zones, by sequencing three maternally inherited chloroplast DNAs (cpDNA: trnL-trnF, psbA-trnH, and rbcL) and the biparentally inherited nuclear DNA (nuDNA: LEAFY) from 19 natural populations of R. chinensis as well as the ecological niche modeling. In all, 23 chloroplast haplotypes (M1–M23) and 15 nuclear alleles (N1–N15) were detected. The estimation of divergence time showed that the most recent common ancestor dated at 4.2 ± 2.5 million years ago (Mya) from cpDNA, and the initial divergence of genotypes occurred at 4.8 ± 3.6 Mya for the nuDNA. Meanwhile, the multimodality mismatch distribution curves and positive Tajima’s D values indicated that R. chinensis did not experience population expansion after the last glacial maximum. Besides, our study was also consistent with the hypothesis that most refugia in the temperate and subtropical zones of China were in situ during the glaciation.
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Affiliation(s)
- Yukang Liang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yang Zhang
- Natural History Research Center, Shanghai Natural History Museum, Branch of Shanghai Science and Technology Museum, Shanghai, China
| | - Jun Wen
- School of Life Science, Shanxi University, Taiyuan, China.,Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Xu Su
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibetan Plateau in Qinghai Province, School of Life Science, Qinghai Normal University, Xining, China
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, China
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Volis S, Fogel K, Tu T, Sun H, Zaretsky M. Evolutionary history and biogeography of Mandragora L. (Solanaceae). Mol Phylogenet Evol 2018; 129:85-95. [DOI: 10.1016/j.ympev.2018.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/11/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
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Manish K, Pandit MK. Geophysical upheavals and evolutionary diversification of plant species in the Himalaya. PeerJ 2018; 6:e5919. [PMID: 30425898 PMCID: PMC6228543 DOI: 10.7717/peerj.5919] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
The Himalaya is one of the youngest and the loftiest mountain chains of the world; it is also referred to as the water tower of Asia. The Himalayan region harbors nearly 10,000 plant species constituting approximately 2.5% of the global angiosperm diversity of which over 4,000 are endemics. The present-day Himalayan flora consists of an admixture of immigrant taxa and diversified species over the last 40 million years. The interesting questions about the Himalayan flora discussed here are: how did the Himalaya achieve high endemic plant diversity starting with immigrant taxa and what were the main drivers of this diversity? This contribution aims to answer these questions and raise some more. We review and analyze existing information from diverse areas of earth and climate sciences, palaeobiology and phytogeography to evolve a bio-chronological record of plant species divergence and evolution in the Himalaya. From the analysis we infer the effects of major environmental upheavals on plant diversity in the region. The understanding developed in the following discussion is based on the idea that Himalaya experienced at least five phases of major geophysical upheavals, namely: (i) mega-collision between India and Eurasian plates, (ii) tectonic uplift in phases and progressive landform elevation, (iii) onset of southwest (SW) Indian monsoon, (iv) spurring of arid conditions in Central Asia, and (v) cyclic phases of cooling and warming in the Quaternary. The geophysical upheavals that were potentially disrupting for the ecosystem stability had a key role in providing impetus for biological diversification. The upheavals produced new geophysical environments, new ecological niches, imposed physical and physiological isolation barriers, acted as natural selection sieves and led to the formation of new species. This contribution aims to develop a comprehensive understanding of the plant biodiversity profile of the Himalaya in the context of complex, interconnected and dynamic relationship between earth system processes, climate and plant diversity.
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Affiliation(s)
- Kumar Manish
- Department of Environmental Studies, University of Delhi, Delhi, India.,Department of Environmental Studies, Dr. Bhim Rao Ambedkar College, University of Delhi, Delhi, India.,Centre for Interdisciplinary Studies of Mountain and Hill Environment, University of Delhi, Delhi, India
| | - Maharaj K Pandit
- Department of Environmental Studies, University of Delhi, Delhi, India.,Centre for Interdisciplinary Studies of Mountain and Hill Environment, University of Delhi, Delhi, India
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Sun Y, Abbott RJ, Lu Z, Mao K, Zhang L, Wang X, Ru D, Liu J. Reticulate evolution within a spruce (
Picea
) species complex revealed by population genomic analysis. Evolution 2018; 72:2669-2681. [DOI: 10.1111/evo.13624] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 10/05/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Yongshuai Sun
- Key Laboratory for Bio‐resource and Eco‐environment of Ministry of Education, College of Life SciencesSichuan University Chengdu 610065 P. R. China
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla 666303 P. R. China
| | - Richard J. Abbott
- School of BiologyUniversity of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla 666303 P. R. China
| | - Kangshan Mao
- Key Laboratory for Bio‐resource and Eco‐environment of Ministry of Education, College of Life SciencesSichuan University Chengdu 610065 P. R. China
| | - Lei Zhang
- Key Laboratory for Bio‐resource and Eco‐environment of Ministry of Education, College of Life SciencesSichuan University Chengdu 610065 P. R. China
| | - Xiaojuan Wang
- Key Laboratory for Bio‐resource and Eco‐environment of Ministry of Education, College of Life SciencesSichuan University Chengdu 610065 P. R. China
| | - Dafu Ru
- Key Laboratory for Bio‐resource and Eco‐environment of Ministry of Education, College of Life SciencesSichuan University Chengdu 610065 P. R. China
| | - Jianquan Liu
- Key Laboratory for Bio‐resource and Eco‐environment of Ministry of Education, College of Life SciencesSichuan University Chengdu 610065 P. R. China
- State Key Laboratory of Grassland Agro‐Ecosystem, Institute of Innovation Ecology & College of Life ScienceLanzhou University Lanzhou 730000 Gansu P. R. China
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Xia M, Tian Z, Zhang F, Khan G, Gao Q, Xing R, Zhang Y, Yu J, Chen S. Deep Intraspecific Divergence in the Endemic Herb Lancea tibetica (Mazaceae) Distributed Over the Qinghai-Tibetan Plateau. Front Genet 2018; 9:492. [PMID: 30429869 PMCID: PMC6220444 DOI: 10.3389/fgene.2018.00492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022] Open
Abstract
Qinghai-Tibetan Plateau (QTP) is an important biodiversity hub, which is very sensitive to climate change. Here in this study, we investigated genetic diversity and past population dynamics of Lancea tibetica (Mazaceae), an endemic herb to QTP and adjacent highlands. We sequenced chloroplast and nuclear ribosomal DNA fragments for 429 individuals, collected from 29 localities, covering their major distribution range at the QTP. A total of 19 chloroplast haplotypes and 13 nuclear genotypes in two well-differentiated lineages, corresponding to populations into two groups isolated by Tanggula and Bayangela Mountains. Meanwhile, significant phylogeographical structure was detected among sampling range of L. tibetica, and 61.50% of genetic variations was partitioned between groups. Gene flow across the whole region appears to be restricted by high mountains, suggesting a significant role of geography in the genetic differences between the two groups. Divergence time between the two lineages dated to 8.63 million years ago, which corresponded to the uplifting of QTP during the late Miocene and Pliocene. Ecological differences were found between both the lineages represent species-specific characteristics, sufficient to keep the lineages separated to a high degree. The simulated distribution from the last interglacial period to the current period showed that the distribution of L. tibetica experienced shrinkage and expansion. Climate changes during the Pleistocene glacial-interglacial cycles had a dramatic effect on L. tibetica distribution ranges. Multiple refugia of L. tibetica might have remained during the species history, to south of the Tanggula and north of Bayangela Mountains, both appeared as topological barrier and contributed to restricting gene flow between the two lineages. Together, geographic isolation and climatic factors have played a fundamental role in promoting diversification and evolution of L. tibetica.
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Affiliation(s)
- Mingze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zunzhe Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Gulzar Khan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qingbo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yu Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
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Jia DR, Bartish IV. Climatic Changes and Orogeneses in the Late Miocene of Eurasia: The Main Triggers of an Expansion at a Continental Scale? FRONTIERS IN PLANT SCIENCE 2018; 9:1400. [PMID: 30319668 PMCID: PMC6167526 DOI: 10.3389/fpls.2018.01400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
Migrations from the Qinghai-Tibetan Plateau (QTP) to other temperate regions represent one of the main biogeographical patterns for the Northern Hemisphere. However, the ages and routes of these migrations are largely not known. We aimed to reconstruct a well-resolved and dated phylogeny of Hippophae L. (Elaeagnaceae) and test hypothesis of a westward migration of this plant out of the QTP across Eurasian mountains in the Miocene. We produced two data matrices of five chloroplast DNA (cpDNA) and five nuclear DNA markers for all distinct taxa of Hippophae. These matrices were used to reconstruct phylogenetic relationships in the genus. In dating analyses, we first estimated the stem node age of Elaeagnaceae using five fossil records evenly distributed across a tree of Rosales. We used this estimate and two fossil records to calibrate the cpDNA and nDNA phylogenies of Hippophae. The same phylogenies were used to reconstruct ancestral areas within the genus. The monophyly of Hippophae, all five species, and most of subspecies was strongly supported by both plastid and nuclear data sets. Diversification of Hippophae likely started in central Himalayas/southern Tibet in the early Miocene and all extant distinct species had probably originated by the middle Miocene. Diversification of Hippophae rhamnoides likely started in the late Miocene east of the QTP from where this species rapidly expanded to central and western Eurasia. Our findings highlight the impact of different stages in uplift of the QTP and Eurasian mountains and climatic changes in the Neogene on diversification and range shifts in the highland flora on the continent. The results provide support to the idea of an immigration route for some European highland plants from their ancestral areas on the QTP across central and western mountain ranges of Eurasia in the late Miocene.
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Affiliation(s)
- Dong-Rui Jia
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czechia
- Department of Genetic Ecology, Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
| | - Igor V. Bartish
- Department of Genetic Ecology, Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
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Wang P, Yao H, Gilbert KJ, Lu Q, Hao Y, Zhang Z, Wang N. Glaciation-based isolation contributed to speciation in a Palearctic alpine biodiversity hotspot: Evidence from endemic species. Mol Phylogenet Evol 2018; 129:315-324. [PMID: 30218774 DOI: 10.1016/j.ympev.2018.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/31/2018] [Accepted: 09/06/2018] [Indexed: 10/28/2022]
Abstract
Organisms are unevenly distributed on earth and the evolutionary drivers of that have puzzled ecologists and evolutionary biologists for over a century. Even though many studies have focused on the mechanisms of unevenly distributed fauna and flora, there remains much to learn about the evolutionary drivers behind biodiversity hotspots. In the Tibetan Plateau and Hengduan Mountains, a biodiversity hotspot in the Palearctic realm, alpine uplift cannot be the driver for recent speciation (<two million years ago), researchers broadly refer to climatic oscillations driven biodiversity, however, the specific individual roles of glaciation and inter-glaciation periods in promoting biodiversity is unclear. The current study focuses on investigating whether recent speciation between two close-related avian species (White eared pheasant, Crossoptilon crossoptilon and Tibetan eared pheasant, C. harmani) was driven by glaciation-based isolation or by dispersal during inter-glaciation. To answer this question, we combined Sanger sequencing and next-generation sequencing technology to estimate population structure, phylogeny, divergence time, demographic history and potential historical distributions for C. crossoptilon and C. harmani, which are endemic to China. We found that the divergence time between these two species and within C. crossoptilon are both during glaciation periods. During glaciation periods, both C. harmani and C. crossoptilon experienced isolated distributions and extreme bottlenecks. The results of this study suggest that glaciation-based isolation contributed to recent speciation in the Tibetan Plateau and Hengduan Mountains, and sheds light on our understanding of the evolutionary mechanisms that contributed to the formation of Palearctic alpine biodiversity hotspots and unevenly distributed species richness pattern.
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Affiliation(s)
- Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Hongyan Yao
- School of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Kadeem J Gilbert
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Qi Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yu Hao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China.
| | - Nan Wang
- School of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China.
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Uplift and denudation in the continental area of China linked to climatic effects: evidence from apatite and zircon fission track data. Sci Rep 2018; 8:9546. [PMID: 29934553 PMCID: PMC6015080 DOI: 10.1038/s41598-018-27801-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/08/2018] [Indexed: 11/29/2022] Open
Abstract
Approximately 2284 fission track data were collected to draw a fission track thermotectonic image of the continental area of China. The result exhibits features such that apatite fission track ages increase from the southwestern to eastern and northern continental areas of China. Thermal paths also reveal the different uplift/denudation processes and times between different tectonic units. At the same time, tectonic uplift of the continent has been among the causes of climate change in the continent since the Cenozoic. The uplift of the Qinghai-Tibet Plateau since the Oligocene is the main cause of the formation of the Asian monsoon and inland droughts, and rapid uplift of the Tibet Plateau after the Pliocene has changed the atmospheric circulation. The main period of climate aridity in Central Asia was caused by the rapid uplift of the Tianshan Mountains since the Miocene, and rapid uplift during the Late Miocene to Pliocene intensified the process of aridity. This study provides the first thermotectonic image of uplift and denudation in the continental area of China and provides a new dating of the formation of the Asian monsoon and climate aridity in Central Asia.
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Su T, Spicer RA, Li SH, Xu H, Huang J, Sherlock S, Huang YJ, Li SF, Wang L, Jia LB, Deng WYD, Liu J, Deng CL, Zhang ST, Valdes PJ, Zhou ZK. Uplift, climate and biotic changes at the Eocene–Oligocene transition in south-eastern Tibet. Natl Sci Rev 2018; 6:495-504. [PMID: 34691898 PMCID: PMC8291530 DOI: 10.1093/nsr/nwy062] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/31/2018] [Accepted: 06/03/2018] [Indexed: 11/29/2022] Open
Abstract
The uplift history of south-eastern Tibet is crucial to understanding processes driving the tectonic evolution of the Tibetan Plateau and surrounding areas. Underpinning existing palaeoaltimetric studies has been regional mapping based in large part on biostratigraphy that assumes a Neogene modernization of the highly diverse, but threatened, Asian biota. Here, with new radiometric dating and newly collected plant-fossil archives, we quantify the surface height of part of the south-eastern margin of Tibet in the latest Eocene (∼34 Ma) to be ∼3 km and rising, possibly attaining its present elevation (3.9 km) in the early Oligocene. We also find that the Eocene–Oligocene transition in south-eastern Tibet witnessed leaf-size diminution and a floral composition change from sub-tropical/warm temperate to cool temperate, likely reflective of both uplift and secular climate change, and that, by the latest Eocene, floral modernization on Tibet had already taken place, implying modernization was deeply rooted in the Palaeogene.
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Affiliation(s)
- Tao Su
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Paleobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Robert A Spicer
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- School of Environment, Earth and Ecosystem Sciences, The Open University, MK7 6AA, UK
| | - Shi-Hu Li
- Guangdong Provincial Key Laboratory of Geodynamics and Geohazards, School of Earth Sciences and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - He Xu
- Institute of Geology and Paleontology, Linyi University, Linyi 276000, China
| | - Jian Huang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Sarah Sherlock
- School of Environment, Earth and Ecosystem Sciences, The Open University, MK7 6AA, UK
| | - Yong-Jiang Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Shu-Feng Li
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Li Wang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Lin-Bo Jia
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Wei-Yu-Dong Deng
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Cheng-Long Deng
- State Key Laboratory of Lithospheric Evolution, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Shi-Tao Zhang
- Faculty of Land Resource Engineering, Kunming University of Science and Technology, Kunming 650093, China
| | - Paul J Valdes
- School of Geographical Sciences and Cabot Institute, University of Bristol, Bristol, BS8 1TH, UK
| | - Zhe-Kun Zhou
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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Gone with the trees: Phylogeography of Rhodiola sect. Trifida (Crassulaceae) reveals multiple refugia on the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2018; 121:110-120. [DOI: 10.1016/j.ympev.2018.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/31/2017] [Accepted: 01/02/2018] [Indexed: 11/23/2022]
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Wang B, Nishikawa K, Matsui M, Nguyen TQ, Xie F, Li C, Khatiwada JR, Zhang B, Gong D, Mo Y, Wei G, Chen X, Shen Y, Yang D, Xiong R, Jiang J. Phylogenetic surveys on the newt genus Tylototriton sensu lato (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts. PeerJ 2018; 6:e4384. [PMID: 29576937 PMCID: PMC5853667 DOI: 10.7717/peerj.4384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato, distributed across the mountain ranges of southeastern Asia. Gene-tree and species-tree analyses of two mitochondrial genes and two nuclear genes revealed five major clades in the genus, and suggested several cryptic species. Dating estimates suggested that the genus originated in the early-to-middle Miocene. Under different species delimitating scenarios, diversification analyses with birth-death likelihood tests indicated that the genus held a higher diversification rate in the late Miocene-to-Pliocene era than that in the Pleistocene. Ancestral area reconstructions indicated that the genus originated from the northern Indochina Peninsula. Accordingly, we hypothesized that the Miocene Climatic Transition triggered the diversification of the genus, and the reinforcement of East Asian monsoons associated with the stepwise uplifts of the Tibetan Plateau promoted the radiation of the genus in southeastern Asia during the Miocene-to-Pliocene period. Quaternary glacial cycles likely had limited effects on speciation events in the genus, but mainly had contributions on their intraspecific differentiations.
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Affiliation(s)
- Bin Wang
- 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, Sichuan, China
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Feng Xie
- 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, Sichuan, China
| | - Cheng Li
- 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, Sichuan, China
| | - Janak Raj Khatiwada
- 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, Sichuan, China
| | - Baowei Zhang
- College of Life Science, Anhui University, Hefei, China
| | - Dajie Gong
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Yunming Mo
- Natural History Museum of Guangxi, Nanning, China
| | - Gang Wei
- Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
| | - Xiaohong Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Youhui Shen
- College of Life Science, Hunan Normal University, Changsha, China
| | - Daode Yang
- Institute of Wildlife Conservation, Central South University of Forestry & Technology, Changsha, China
| | - Rongchuan Xiong
- Department of Life Science, Liupanshui Normal University, Liupanshui, China
| | - Jianping 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, Sichuan, China
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