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Phylogeny of the Stipa and Implications for Grassland Evolution in China: Based on Biogeographic Evidence

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Phylogeny of the Stipa and Implications for Grassland Evolution in China: Based on Biogeographic Evidence Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-140 Manuscript under review for journal Biogeosciences Discussion started: 26 April 2018 c Author(s) 2018. CC BY 4.0 License. Phylogeny of the Stipa and implications for grassland evolution in China: based on biogeographic evidence 1 Qing Zhang1*, Junjun Chen1, Yong Ding2 2 1 School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, 3 China 4 2 Grassland Research Institute of Chinese Academy of Agricultural Sciences, Hohhot, 5 010010, China; 6 * Corresponding author. Email: [email protected] 7 8 Abstract 9 The evolution of Chinese grassland is a still an important question biogeography. In this study, the 10 phylogeny of 20 Stipa species (extensively distributed in Chinese grassland) was established to 11 explore the origin and dispersal routes of Chinese grassland. It showed that Stipa species 12 originated at 28 MaBP and they started to differentiate in central Inner Mongolia at 22 MaBP. 13 Then, Stipa species expanded along four routes: (1) they expanded from central Mongolia to the 14 Qilian Mountains, Qinghai, and western Tibet at 16 MaBP. They then gradually expanded from 15 western to eastern Tibet from 11-6 MaBP. (2) At 12 MaBP, they expanded from central Inner 16 Mongolia to the Helan Mountains. (3) At 8 MaBP, they expanded from central Inner Mongolia to 17 the Xinjiang area. (4) At 4 MaBP, they expanded from central to eastern Inner Mongolia. 18 Therefore, we could deduce the formation order of Chinese grasslands: central Inner Mongolia > 19 Qilian Mountains > Qinghai > western Tibet > Helan Mountains > Xinjiang > central Tibet > 20 eastern Tibet > eastern Inner Mongolia. We highlight the importance of the uplift of the 21 Qinghai-Tibet Plateau and paleoclimate changes in triggering the origin and evolution of Stipa 22 species and Chinese grasslands. 23 Keywords: uplift of the Qinghai-Tibet Plateau; paleoclimate; explosive radiation; 24 phylogeny 1 Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-140 Manuscript under review for journal Biogeosciences Discussion started: 26 April 2018 c Author(s) 2018. CC BY 4.0 License. 25 26 1 Introduction 27 Different regions on earth harbor distinct biological species even though their 28 environment are the same, indicating that the distribution of organisms not only is 29 driven by contemporary ecological factors but may also be closely associated with 30 historical factors (e.g., geological evolutionary history and population evolutionary 31 history) (Medail and Diadema, 2009; Ordonez and Svenning, 2015; Santos et al., 32 2017). Based on molecular clocks, the genetic information of existing species could 33 be used to explore the biogeographic processes including the origin, divergence, 34 expansion, and isolation of organisms at the molecular level during all important 35 geological history events. In addition, the time of divergence between closely related 36 species could be basically confirmed (Tedesco et al., 2017; Voskamp et al., 2017; 37 Wang et al., 2017a). 38 Grasslands are an important component of the global ecosystem and provide 39 significant ecosystem functioning and service.. One sixth total land area is covered by 40 grassland (Scurlock and Hall, 1998). The Chinese grasslands, starting from the 41 Northeast China Plain, Inner Mongolian Plateau, Ordos Plateau, and Loess Plateau to 42 the southern margin of the Qinghai-Tibet Plateau, are major part of the Eurasian 43 Steppe, which is the world’s largest grassland (Addison and Greiner, 2016; Wu et al., 44 2015). The Chinese grasslands are of great interests in ecological studies, including 45 grassland biodiversity (Buergi et al., 2015; Yuan et al., 2016), community assembly 46 (Li and Wu, 2016; Niu et al., 2016), stoichiometry (Wang et al., 2017b), and 47 ecosystem function (Jing et al., 2015; Mao et al., 2017). Meanwhile, a few studies 48 have also discussed the origin and dispersal routes of Chinese grassland genus (Favre 49 et al., 2016; Luo et al., 2016). However, the formation and evolutionary processes of 50 Chinese grasslands are still rarely studied. 51 According to paleogeographical climate change, Chinese grasslands might first 52 emerge in the late of the Tertiary Period because of the global cooling and 53 aridification (Wu et al., 2015). In addition, Meang and McKenna (1998) found that 54 perissodactyl-dominant faunas of the Eocene were abruptly replaced by 2 Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-140 Manuscript under review for journal Biogeosciences Discussion started: 26 April 2018 c Author(s) 2018. CC BY 4.0 License. 55 rodent/lagomorph-dominant faunas of the Oligocene in Mongolia Plateau at 33 MaBP, 56 similar to the European Grande Coupure. And they think the turnovers were mainly 57 driven by global climatic shifts and prominent biotic reorganization from forest to 58 grassland. Based on the evidence of sporopollen, more studies focused on vegetation 59 shift and climate change in steppe area of China during the mid-late Holocene 60 (Mischke et al., 2016; Shen et al., 2008). These studies are of great importance for 61 revealing the origin and evolution of Chinese grasslands. However, they were mainly 62 based on a certain history period, and did not explain the expansion routes of Chinese 63 grasslands. We need more direct evidence to obtain a comprehensive and continuous 64 history of grassland evolution. Based on currently molecular information, which 65 providing more accurate and direct evidence for the evolutionary process, 66 biogeography can be used to deduce the origin and expansion routes of Chinese 67 grasslands and to explore the effects of important geological historical events (Favre 68 et al., 2016; Ferreira et al., 2017). 69 Although Chinese grasslands is vast and covers different vegetation types, Stipa 70 species are dominant through the whole Eurasian steppe, including Chinese 71 grasslands (Durka et al., 2013; Hamasha et al., 2012). Because of differences in 72 climate, Stipa species show obvious zonal distribution characteristics in Chinese 73 grasslands. Stipa baicalensis, Stipa grandis, and Stipa krylovii are constructive 74 species in the typical grasslands; Stipa tianschanica and Stipa glareosa are distributed 75 extensively in the desert steppe; and Stipa purpurea has a very extensive distribution 76 in alpine steppes. In addition, Stipa basiplumosa and Stipa subsessiliflora are also 77 distributed in the high mountains of desert areas (Durka et al., 2013; Wu et al., 2015). 78 Therefore, Stipa species play very important roles in the formation of Chinese 79 grasslands. The evolutionary processes of Chinese grasslands are closely related to the 80 evolution of Stipa species. Studies on the history of origin, divergence and expansion 81 routes of Stipa species are an excellent indicator to reveal the evolution of Chinese 82 grasslands. Therefore, in this study, Stipa species that were distributed extensively in 83 different grassland areas including Inner Mongolia, Qinghai, Tibet, and Xinjiang were 84 collected. The four gene fragments of chloroplasts, matk, rbcl, trnh-psba, and trnl-f, 3 Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-140 Manuscript under review for journal Biogeosciences Discussion started: 26 April 2018 c Author(s) 2018. CC BY 4.0 License. 85 were selected to estimate the divergence time tree of Stipa species using BEAST 86 (Bayesian evolutionary analysis by sampling trees). In addition, the origin, divergence 87 and expansion routes of Stipa species were reconstructed based on RASP 88 (Reconstruct Ancestral State in Phylogenies). Finally, the origin and evolutionary 89 processes of Chinese grasslands were deduced and the effects of paleoclimate and 90 geological historical events were further explored. 91 92 2 Materials and Methods 93 2.1 Materials 94 This study contained 20 species of Stipa species collected from seven different 95 grasslands area (Fig 1, Table 1). Helictotrichon schellianum, Achnatherum splendens, 96 and Ptilagrostis pelliotii, which are closely related to Stipa species, were used as the 97 outgroup (Hamasha et al., 2012). Considering there is certain hybridization between 98 Stipa species(Gonzalo et al., 2012), nuclear-derived markers were not employed, and 99 the four gene fragments of chlorophyll, matk, rbcl, trnh-psba, and trnl-f, were used for 100 analyses. 101 2.2 Methods 102 2.2.1 Total DNA extraction, PCR amplification, and sequencing 103 This study performed total DNA extraction using the Plant Genome Extraction 104 Kit (Tiangen Biotech,Beijing, China). DNA samples were diluted to 30 ng/μL for 105 future use(Ramirez et al., 2017). The four selected gene fragments were amplified by 106 PCR. The universal primers were acquired from previous studies (Durka et al., 2013; 107 Hamasha et al., 2012; Ren et al., 2011). The PCR reaction volume was 50 μL; 108 specifically, 2 μL of DNA template, 2 μL each of upstream and downstream primers, 109 25 μL of 2× PfuUltra Master Mix, and 24 μL ddH2O were combined (Lu et al., 2013). 110 The matk gene amplification was carried out using the following procedure: 111 pre-denaturation at 94°C for 5 min; 30 cycles of denaturation at 94°C for 30 s, 112 annealing at 40°C for 30 s, and extension at 72°C for 1 min; and a final extension at 113 72°C for 10 min. The same amplification procedure was used for the trnh-psba 114 sequence. For the amplification of trnl-f and rbcl, the annealing temperatures were 4 Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-140 Manuscript under review for journal Biogeosciences Discussion started: 26 April 2018 c Author(s) 2018. CC BY 4.0 License. 115 changed to 57°C and 52°C , respectively, and the other conditions remained 116 unchanged. The amplification products were subjected to 1% agarose gel 117 electrophoresis and sent to the Beijing Genomics Institute for sequencing when the 118 samples were ready. 119 2.2.2 Sequence comparison 120 The molecular data obtained from sequencing were assembled using BioEdit and 121 compared using ClustalW.
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