This paper summarizes the research status, existing issues, and trends in floristic geography. There is now a wealth of research accumulation on floristic investigations, distribution types of genera, floristic regions, and regional floristic analysis. It is also noted that most of these studies utilize simple statistical analyses, comparative studies, traditional methods, and single subjects, to provide a basic understanding and description of the floristic phenomenon, which is lacking spatial pattern formation processes and detailed exploration of formation mechanisms. Additionally, there are still some weak and non-existent areas of botanical investigation. Many existing specimens lack detailed or accurate information and the precise identification of plant species also needs to be much improved. At the same time, when analyzing the development trends of floristic geography, with the rapid development of related disciplines, including the development of biogeography and analysis methods and improvements, floristic geography research is an area of multidisciplinary integration, comprehensive research, and analysis. On the one hand, using database information, and combining ecology, paleobotany, and geology can allow us to probe into spatial pattern formation. On the other hand, combining phylogenetics, the tree of life, and molecular biogeography allow us to reveal floristic origins and evolution. The rapid development of various disciplines has given rise to a large amount of data, meanwhile, the emergence and application of new analytical methods and theories incorporate big data into floristic geography research, which will enhance qualitative understanding and description, and allow us to further explore the mechanisms of formation quantitatively.

Geological events are one of the critical factors that are responsible for the formation and development of regional flora. Major geological events are discussed in this article with an emphasis on their impacts on dominant elements of evergreen broad-leaved forests, as well as on relict and endemic elements of Chinese flora. Geological events contributing to the complex geological history of China include the Paloecene-Eocene Thermal Maximum (PETM), the uplifting of the Qinghai-Tibet Plateau, the formation and development of the monsoon climate, and the shifting of dry areas in China during the Cenozoic Era. As rich geological environments are the basis for forming and developing biodiversity, such biodiversity can be seen in the main elements of subtropical evergreen broad-leaved forests, which have been presented in China since the Neogene, and include Fagaceae, Lauraceae, Magnoliaceae, Fabaceae and Hamamelidaceae. The morphological characteristics of these elements are comparable with modern taxa at the genus level. The monsoon climate in China, especially dry winters and springs, strongly impacts floristic patterns. Relict and endemic plants are concentrated in Central China where winter and spring are comparatively humid. Monsoon intensity and development are correlated with the height of the Qinghai-Tibet Plateau.

In this review, based on recent studies of population genetics and phylogeographics of East Asia’s Tertiary relict plants, we have outlined the main phylogeographic patterns and processes. We also summarize common geographic and environmental factors which may contribute to the phylogeographic patterns of East Asia’s Tertiary relict plants and present future challenges and research prospects. There are four recurrent phylogeographic scenarios identified by different case studies, including: (1) the global cooling and aridification during the Middle and Late Miocene induced recent speciation, with climate change during the Late Pliocene and Pleistocene accounting for their intra-specific lineage divergence, genetic diversification and demographic expansion/contraction. The latitudinal contraction/expansion can lead to the formation of “suture zone” for some relict plants; (2) the effects of the formation of the glacial East China Sea land bridge, as a “corridor” or “filter”, have to account not only for habitat preferences per se but also for other biological features of different relict plant species; (3) the uplift of the Qinghai-Tibet Plateau (QTP) during the Late Pliocene and the intensification of East Asian monsoon system (EAMS) are the most suggestive factors responsible for the major phylogeographic break between the western and eastern lineages across the Sichuan Basin and northwestern arid regions; and (4) some Tertiary relict plants migrated southward to Taiwan from mainland China or Japan before the Pleistocene under global climatic cooling and aridification since the Late Miocene, and refugial isolation that occurred between Taiwan and mainland Asia accelerated vicariant lineage diversification and speciation. Overall, both historical and contemporary geography and environment have affected the distribution, genetic diversity, lineage divergence and speciation of East Asia’s Tertiary relict plants. Finally, we emphasize notable gaps in our knowledge due to the long-term application of simple molecular clock based on very limited genetic markers, and outline future research prospects for disentangling the evolution and biogeographic history of East Asia’s Tertiary relict flora. We present the utilization of genome data and biogeography models and integrative phylogeographic research of multi-taxon communities as possible future directions.

A floristic phytogeography of arid regions of northwestern China is outlined in this paper. Most researches of floristic cataloging and phytogeography of families and genera were started since 1980. We propose that Central Asia, as a natural region, should be regarded as a distinct unit to study, namely combining northwestern China, Kazakhstan, Uzbekistan, Kyrgyzstan, Tajikistan and Turkmenistan as one unit. Local research is not sufficient or holistic for study of plant floristics and evolutionary history. We address the significance and potential of molecular phylogeny and biogeography of families and genera. Linking geological and palaeoclimate events, especially the Qinghai-Tibetan Plateau uplift and the Tethys retreat in the historical floristic phytogeography and vegetation, is suggested as they are the main dynamics of Central Asian aridification.

The regional tree of life, reconstructing the tree of life to include the regional species pool, has been a research focus in biological science over the past decade. Informed by phylogenetic relationships among coexisting species, a regional tree of life can connect evolutionary and ecological factors during the evolution of a biota and thus has become an efficient tool to trace its temporal and spatial diversification. In this paper, we summarize the application of a regional tree of life in floristic studies in the following three fields: (1) To reveal temporal patterns of a flora by estimating divergence time and evolutionary rates based on the tree of life; (2) To reveal spatial patterns of the biodiversity in a flora and to guide the regionalization of floristic zones by integrating phylogenetic and spatial data; and (3) By integrating biogeographic and environmental data and investigating how taxa respond to paleogeographic events and thus climate change to reveal the underlying ecological, geographical and historic factors of the formation of the floristic biodiversity pattern. In addition, we highlight the relationship between the regional and global tree of life and indicate the potential to identify biased divergence times with incomplete taxa sampling using a regional tree of life. Finally, we suggest that future studies should integrate current mega data at different scales in hotspots to elucidate biodiversity patterns in a worldwide framework.

The evolution and maintenance of biodiversity is largely determined by the interaction of genetics and environmental factors. Geological and climatic histories, which played pivotal roles in the evolution and maintenance of plant diversity in the Qinghai-Tibet Plateau (QTP) and adjacent regions, are the most important environmental aspects. We review the major effects of QTP environmental changes associated with geological uplift, Asian monsoon evolution, and Pleistocene climatic oscillation on the origin, evolution, population demography, and maintenance mechanisms of plant diversity in the QTP and adjacent regions across spatiotemporal scales. Furthermore, we summarize the current progress and knowledge gaps on mechanisms of diversification and maintenance of plant diversity, and outline the effect of climate change on plant genetic diversity, hybrid zone dynamics, plant diversity patterns, the effect of Asian Monsoon evolution on plant diversity maintenance, and mechanisms of community assembly, the five additional future research hotspots.

The application of phylogenetic relationships helps us to understand species composition and species distribution patterns, which provide a scientific basis for the effective protection and sustainable use of biological diversity. Phylogenetic diversity (PD_faith), based on branch lengths of the phylogenetic tree, is the most basic measurement index. Many indices are derived from PD_faith, which makes difficult to choose the most appropriate parameters. The most effective and feasible way is to select suitable indices based on specific research questions, and some examples have been presented in plant phylofloristics and biodiversity conservation. DNA sequences have rapidly accumulated particularly through the global DNA barcoding project, which provides a standardized mass data, and can be used to reconstruct mega-phylogeny. But studies conducted around the phylogenetic diversity require more information, specifically data on species distribution, environmental factors, and climatic data. In addition, some fundamental questions need to be verified, such as the relationship between phylogenetic diversity and ecosystem functions.

Alpine areas are global biomes with extreme environments and distinct boundaries. Studies on the geography of alpine flora help us to understand the formation of flora in an extremely cold and segregated environment, as well as the floristic relations between mountains. We integrated alpine flora data from 14 main mountain ranges in China, measured floristic similarities using the Jaccard index, and explored the percentage composition of areal-types of seed plants and the effects of geographical distance and environmental variation on flora similarities using correlation analyses and Mantel tests. Results indicated that Chinese alpine zones harbor a flora characterized by high species richness, with 3,670 species (including 340 subspecies units) belonging to 489 genera and 65 families recorded in the alpine zone of 14 main mountain ranges. These genera are mainly constituted of areal-types of North Temperate distribution and their sub-types, Cosmopolitan, Old World Temperate, East Asia and Sino-Himalayan, while the Sino-Japanese type is absent. Those endemic to China revealed a distinct presence in alpine flora (5.2%). Based on the data from 14 alpine zones, geographical patterns of alpine floristic composition were characterized by a significant latitudinal decrease of tropic and East Asia areal-types, and an increase of northern temperate types. Along the longitudinal gradient, the percentages of Mediterranean types decreased while the northern temperate types increased, and East Asian elements peaked in the middle position. The alpine floras of 14 mountains were significantly correlated in terms of geographical element composition when measured at the genus level, revealing two groups of higher floristic correlations, mountains surrounding the Qinghai-Tibet Plateau and separated northern mountains, respectively. The alpine flora of Taiwan Island is more closely related with that of the northern mountains rather than that of the mountains found in Southwest China, which have more comparable latitudes. We found that geographic distance was the primary factor for deviation between alpine floras, while the physiognomy of alpine zones also influenced floristic composition, and the maximum temperature of warmest month (MTWM) was a critical climatic factor for geographical deviation of alpine flora composition in China, which suggests the potential stress effects of global warming on alpine flora.

Traditional attempts of floristic studies typically focus on the analyses of taxonomic composition and areal-types of flora, often ignoring the rich context that evolutionary history can provide. In this study, based on the recent study examining the delineation of floristic regions in Yunnan, by combining data on the distributions and phylogenetic relationships of 1,983 genera of native seed plants, we explore how taxonomic composition, phylogenetic relatedness, and phylogenetic structure vary across the different geographic regions in this area. As predicted, phylogenetic diversity was well correlated with taxonomic diversity among the geographic regions. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Also, phylogenetic relatedness was well correlated with taxonomic composition between geographic regions in Yunnan. Cluster analyses of the similarities of phylogenetic relatedness and taxonomic composition show that geographic regions with tropical floristic affinity form a single cluster separate from another cluster composed of geographic regions with temperate floristic affinity. Our results show that the integration of phylogenetic information can help us to better understand the characteristics and origin of flora.

The Chinese tropical region has generally been recognized to be the area on the northern edge of tropical Asia, and includes southeastern Xizang (Tibet), southern Yunnan, southwestern Guangxi, southern Taiwan, and Hainan Island. Based on present floristic records and data from these tropical areas, 12,844 species of seed plants including 2,181 genera and 227 families, are recognized. The families that are distributed mainly in tropical areas but extended to the temperate zone contribute to the majority of the flora of tropical China, and genera with tropical distributions make up the most of the total flora, which indicate that the flora of tropical areas in China is marginally tropical in nature. The genera with the tropical Asian distribution contributed to the highest portion among the various distribution types, which implies tropical Asian or Indo-Malaysia affinity of the tropical flora of China. The tropical flora of China has conspicuous variations in floristic composition and geographical elements from region to region due to different geological history and ecological environments, although the floristic similarities at the family and generic levels are more than 90% and 64%, respectively but lower than 50% at the specific level, among the compared regional floras from southwestern China and southeastern China. We found that there are more similar dominant families and genera, and also higher similarities between families and genera between southeastern Tibet (Xizang) and southeastern Yunnan. The floras of southern and southeastern Yunnan have a higher portion of the tropical Asian elements compared with other tropical floras in China, and although they have the highest similarity at specific level, the dominant families and genera have conspicuous differences between them. The flora of Hainan has the highest ratio of tropical elements, of which the pan-tropical element has the highest portion. Differences in characteristics and evolution in these tropical floras could be influenced mainly by historical events occurring with uplift of Himalayas, such as the southeastward extrusion of the Indochina geoblock, clockwise rotation and southeastward movement of Lanping-Simao geoblock, divergent geological histories between southern and southeastern Yunnan, and southeastward movement of Hainan Island.

The Qinghai-Tibet Plateau and Hengduan Mountains is an important hotspot to study the origin and evolution of plant biodiversity, which is characterized by high species richness and endemism, as well as a unique location and complicated topography. Based on a comprehensive survey of the chromosome numbers of angiosperms from the Qinghai-Tibet Plateau and Hengduan Mountains, our results indicated that the frequency of neopolyploids (23%) was much lower than expected. This was likely caused by the unique history, geology, and complicated topography and habitat. Another mechanism of chromosomal evolution is on the diploidy level (ca. 43.3%), with variations of chromosomal restructure and karyotype. The number of paleopolyploids (diploids with high base numbers) was large in plants from this mountain area (33.7%). The diversity of chromosomal evolution patterns of angiosperms from this region may be correlated to the high level of species richness and endemism. This study provides useful insight into our understanding of speciation, the origins of alpine flora and other important issues in eastern Asia and other regions in the Northern Hemisphere.