Journal of Systematics and Evolution 9999 (9999): 1–16 (2014) doi: 10.1111/jse.12088 Review Plant phylogeography in arid Northwest China: Retrospectives and perspectives 1,2,3Hong‐Hu MENG† 2,3Xiao‐Yang GAO† 1,3Jian‐Feng HUANG 2,4Ming‐Li ZHANG* 1(Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China) 2(Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China) 3(University of Chinese Academy of Sciences, Beijing 100049, China) 4(Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) Abstract Despite the absence of major Quaternary glaciations in arid Northwest China, significant climatic oscillations definitely impacted the evolution of the biota in situ. Phylogeography has grown as a discipline because it has provided explicit tools for the study of geographical subdivision among populations. But phylogeographical application for arid Northwest China has begun to blossom, which has provided evidence that aridification played a significant role in the increase of genetic diversity and species diversification. The time frame corresponds with Pleistocene climatic oscillations, which caused extreme aridity and the expansion of sandy deserts. In the Asian desert flora subkingdom and Eurasian forest subkingdom of Northwest China, the recurrent phylogeographical scenarios, identified by different case studies, broadly agree with longstanding biogeographic, floristic, and topographic concepts: (i) aridification promoted diversification and speciation of desert plants; (ii) desert expansion caused habitat fragmentation; (iii) the Altay–Tianshan Mountains included glacial refugia for plants; (iv) population expansion and recolonization from glacial refugia occurred during the postglacial period; and (v) desert plants persistence and alpine plants retreat during climate oscillations. We discuss the main phylogeographical findings in light of molecular and paleo‐environmental evidence, emphasizing notable gaps in our knowledge and outlining future research perspectives for disentangling the evolutionary history of this arid region’s flora. Key words arid Northwest China, aridification, phylogeography, Quaternary. With the development of molecular methods, an effective approach, when detailed reconstruction of phylogeography has grown as a popular discipline the evolutionary process of plant species has been investigating geographical variation by use of molecu- hampered by lack of fossil data, to untangle the lar markers, and it has explored explosively in the recent evolutionary history of species (Comes & Kadereit, three decades since 1987 (Avise et al., 1987). At 1998). In documentation of the effects of climatic shifts present, it is well appreciated that global climate on organisms, numerous phylogeographical surveys of fluctuations, in particular the remarkable Quaternary temperate plant species in Europe (e.g., Demesure et al., climatic oscillations, have instigated cycles of habitat 1996; Comes & Kadereit, 1998; Schönswetter et al., contraction and expansion, and latitudinal–altitudinal 2005), North America (e.g., Shaw & Small, 2005; shifts of species’ distributions, affecting the genetic Brunsfeld et al., 2007; Gonzales et al., 2008), and the structure of many plant and animal species in temperate Japanese Archipelago (e.g., Okaura & Harada, 2002; zones of the Northern Hemisphere (Hewitt, 2000, 2004; Ikeda & Setoguchi, 2007) can be referenced. Phylo- Petit et al., 2003; Hickerson et al., 2010). Phylogeog- geography also addressed the topic in South America, raphy has been appreciated as a major focus of Africa, and Australia, where research has seen evolutionary biology, using spatiotemporal distribution exponential growth recently (e.g., Lorenz‐Lemke of genetic lineages to deduce the influence of historical et al., 2010; Lorenzen et al., 2012; Nakamura et al., processes on species’ evolution. Also, it has provided 2012; Segovia et al., 2012). Phylogeographical surveys of plant species have been informative in resolving or further delineating the location of glacial refugia, and Received: 21 November 2013 Accepted: 25 February 2014 routes of colonization and range expansion after glacial † These authors contributed equally to this work. Ã Author for correspondence. E‐mail: [email protected]. Tel.: 86‐ periods (Petit et al., 2003; McLachlan et al., 2005; Ikeda 991‐7885515. Fax: 86‐991‐7885320. & Setoguchi, 2007; Gonzales et al., 2008; Carnicer © 2014 Institute of Botany, Chinese Academy of Sciences 2 Journal of Systematics and Evolution Vol. 9999 No. 9999 2014 et al., 2012). In addition, phylogeographical results, effects (Lu et al., 2004; Clark et al., 2005; Fang et al., regardless of whether pertaining to trees, shrubs, or 2005). In addition to these geologic events, the climate herbs, have proved to be consistent with fossil pollen of temperate areas of the earth experienced a general evidence in indicating extensive latitudinal range shifts, cooling and drying trend connected with atmospheric typically in the form of retreat southward and to lower CO2 decrease (Dupont‐Nivet et al., 2007; Miao et al., altitudes during glaciation, followed by rapid expansion 2012), which reached their most profound minima northward and to higher altitudes during postglacial during glacial periods of the Pleistocene. Strong intervals (Comes & Kadereit, 1998; Hewitt, 1999; episodic cooling at those times resulted in sharp Nason et al., 2002; Sakaguchi et al., 2011; Segovia increases in aridity of the Chinese deserts (Fang et al., 2012; Voss et al., 2012). et al., 2002; Ding et al., 2005). In China, the progress of plant phylogeographical Deserts make up approximately one‐third of studies has been recently outlined (Qiu et al., 2011; Liu Earth’s land surface, and host a surprisingly rich et al., 2012). As pointed out by these authors, most biodiversity. Geological processes, such as the dynam- studies have focused on the Sino‐Japanese flora of East ics of sand movement, oasis formation, and river course Asia, in which harbors the largest amount of diversity alterations, often affect population genetic structure and among the world’s temperate regions (Ying et al., 1993; speciation (Riddle et al., 2000; Nason et al., 2002; Myers et al., 2000); it was also the most important glacial Riddle & Hafner, 2006; Garrick et al., 2009) in deserts refugium for Tertiary representatives (“relics”)through- of North America, Africa, and Australia. Geographic out Quaternary ice‐age cycles (Qiu et al., 2011). Studies barriers between deserts apparently have led to vicariant have often investigated endangered or endemic species, speciation or population differentiation in many desert especially those concentrated in the areas of the organisms (Byrne, 2008; Fehlberg & Ranker, 2009; Hengduan Mountains and adjacent Qinghai–Tibet Rebering et al., 2010). Climatic oscillations and Plateau (QTP) regions (Cun & Wang, 2010; Li et al., associated environmental changes in the Quaternary 2010; Zhang et al., 2011; Jia et al., 2012; Liu et al., 2013; promoted range fragmentation, vicariance, and popula- Wang et al., 2013a; Zhao et al., 2013). These constitute tion isolation, providing opportunities for allopatric an area referred to as the core of the Himalayan hotspot, speciation through the action of selection and/or genetic containing one of the greatest concentrations of drift in temperate plants. So far, a growing body of biodiversity in the world due to its high level of species studies, based on pollen cores, fossils, moraines, and and generic richness. In contrast, very few studies have deposition of loess, have begun to elucidate the possible been applied to the vegetation in arid zones of China. roles of geology, multiple glaciations and climatic Development of deserts in Central Asia was a oscillations in shaping the current geo‐ecological response to global climatic change (e.g., long‐term system occurring across these arid zones (Sun, 2002; cooling and drying trends) and regional factors (e.g., the Wu et al., 2002; Sun & Zhang, 2009; Sun et al., 2010; environmental effects of the Himalayas and QTP Guan et al., 2011). However, phylogeography of plant rising). The India–Asia continental collision may species spanning the arid zones of Northwest China are have begun at ca. 50 Mya; uplift had become sufficient limited and, to the best of our knowledge, restricted to by late Eocene or early Oligocene for the appearance of regional floras. Thus, a phylogeographical review on abundant pollen of high altitude conifers in the north of arid Northwest China is now needed. the QTP and in sediments of the South China Sea (Wu Our focus is on the effects of Quaternary changes et al., 2003; Hoorn et al., 2012). Retreat of the Tethys in climate and topography on the current population Ocean from the Tarim Basin also occurred at that time genetic structure of plants in these regions, especially in (Hoorn et al., 2012). A consequent increase in arid light of region‐specific paleo‐environmental evidence, Eurasian continental interior is demonstrated by the first but also considering major phylogeographical concepts appearance of pollen referable to Artemisia L., as well developed in other temperate regions of the Northern as abundant chenopods (Sun & Wang, 2005; Miao Hemisphere. We begin with a brief account of the et al., 2011; Hoorn et al., 2012). By the early Miocene, phytogeographic