Tibet, the Himalaya, Asian monsoons and biodiversity - In what ways are they related?

The origin and morphological character evolution of the paleotropical woody bamboos

The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and time-calibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing, and explored the evolutionary trends of habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene-Miocene boundary and formed four major clades, that is, Melocanninae, Racemobambosinae s.l. (comprising Dinochloinae, Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l. (comprising Bambusinae s.str. plus Holttumochloinae). The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.

Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae)

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.

Plastid phylogenomics provides new insights into the systematics, diversification, and biogeography of Cymbidium (Orchidaceae)

Cymbidium (Orchidaceae: Epidendroideae), with around 60 species, is widely-distributed across Southeast Asia, providing a nice system for studying the processes that underlie patterns of biodiversity in the region. However, phylogenetic relationships of Cymbidium have not been well resolved, hampering investigations of species diversification and the biogeographical history of this genus. In this study, we construct a plastome phylogeny of 56 Cymbidium species, with four well-resolved major clades, which provides a framework for biogeographical and diversification rate analyses. Molecular dating and biogeographical analyses show that Cymbidium likely originated in the region spanning northern Indo-Burma to the eastern Himalayas during the early Miocene (∼21.10 Ma). It then rapidly diversified into four major clades in East Asia within approximately a million years during the middle Miocene. Cymbidium spp. migration to the adjacent regions (Borneo, Philippines, and Sulawesi) primarily occurred during the Pliocene-Pleistocene period. Our analyses indicate that the net diversification rate of Cymbidium has decreased since its origin, and is positively associated with changes in temperature and monsoon intensity. Favorable hydrothermal conditions brought by monsoon intensification in the early Miocene possibly contributed to the initial rapid diversification, after which the net diversification rate was reduced with the cooling climate after the middle Miocene. The transition from epiphytic to terrestrial habits may have enabled adaptation to cooler environments and colonization of northern niches, yet without a significant effect on diversification rates. This study provides new insights into how monsoon activity and temperature changes affected the diversification dynamics of plants in Southeast Asia.

Meta-analysis provides insights into the origin and evolution of East Asian evergreen broad-leaved forests

Evergreen broad-leaved forests (EBLFs) are dominated by a monsoon climate and form a distinct biome in East Asia with notably high biodiversity. However, the origin and evolution of East Asian EBLFs (EAEBLFs) remain elusive despite the estimation of divergence times for various representative lineages. Using 72 selected generic-level characteristic lineages, we constructed an integrated lineage accumulation rate (LAR) curve based on their crown ages. According to the crown-based LAR, the EAEBLF origin was identified at least as the early Oligocene (c. 31.8 million years ago (Ma)). The accumulation rate of the characteristic genera peaked at 25.2 and 6.4 Ma, coinciding with the two intensification periods of the Asian monsoon at the Oligocene - Miocene and the Miocene - Pliocene boundaries, respectively. Moreover, the LAR was highly correlated with precipitation in the EAEBLF region and negatively to global temperature, as revealed through time-lag cross-correlation analyses. An early Oligocene origin is suggested for EAEBLFs, bridging the gap between paleobotanical and molecular dating studies and solving conflicts among previous estimates based on individual representative lineages. The strong correlation between the crown-based LAR and the precipitation brought about by the Asian monsoon emphasizes its irreplaceable role in the origin and development of EAEBLFs.

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

Disentangling the effects of geographic distance, environment and history on beta diversity of freshwater fish at a biogeographical crossroads

Examining assemblage turnover and variation along geographic and environmental distances is a useful approach to evaluate beta diversity patterns and associated driving mechanisms. However, such studies are relatively limited in freshwater systems. Here, we compared the relationships between freshwater fish beta diversity and geographic distances among 165 hydrological units (HUs) in four zoogeographical regions (PA, Palearctic Region; CA, High Central Asia; EA, East Asia, SA, South Asia) across China and adjacent areas. This area can be considered a biogeographical crossroads, where faunal composition shares elements with different biogeographic and evolutionary origins. We found a considerably high level of between-HU overall dissimilarity (βsor, range from ca. 0.60 to 0.85) in all four regions, mainly due to the turnover component (the relative contribution of βsim to βsor ranged from 60% to 90%). In general, βsor and βsim both significantly increased with geographic distance (except in PA), whereas the nestedness-resultant component (βsne) decreased with geographic distance. The intercepts and slopes of the relationships between dissimilarities and distance (RDDs) both varied significantly among the four regions. The intercepts of βsor and βsim were both highest in SA, followed by CA, PA and EA, implying different levels of fish faunal heterogeneity at short distances. In contrast, the slopes of these two dissimilarities followed the decreasing trend from EA > CA > SA > PA, suggesting different environmental suitability and dispersal ability of fish species among regions. Variation partitioning in distance-based redundancy analysis showed that the spatial and historical factors were more important than area-heterogeneity and energy factors across all HUs and within three individual ecoregions (EA, SA and CA), but spatial factors were non-significant in PA. Our study highlighted the usefulness of RDDs in understanding biogeographical patterns and enhancing the biodiversity conservation of freshwater fishes.

Indian monsoon drove the dispersal of the thoracica group of Scytodes spitting spiders

We examined the global biogeography of the Scytodes thoracica group of spitting spiders based on 23 years of sampling at the species level (61 species in the thoracica group and 84 species of Scytodes) using DNA data from six loci. Our results indicated that the thoracica group initially dispersed from Southeast Asia to East Africa between 46.5 and 33.0 million years ago, and dispersal events intensified between Southeast/South Asia and East/South Africa from the early to late Miocene. The timing of these events indicates that Asian-African faunal exchange of the thoracica group was driven by the Indian monsoon, and the pattern of dispersal suggests that colonialization took root when the Indian monsoon shifted from a North-South direction to an East-West direction from the middle Eocene.

The Sino-Himalayan flora evolved from lowland biomes dominated by tropical floristic elements

BACKGROUND

The Sino-Himalayan flora harbors highly diverse high-elevation biotas, but our understanding of its evolutionary history in temporal and spatial dimensions is limited. In this study, we integrated a dated phylogenetic tree with comprehensive species distribution data to investigate changes over time and space in floristic elements, including the tropical, Tethys, northern temperate, and East Asian floristic elements, across the entire Sino-Himalaya and its three floristic regions: the Yunnan Plateau, Hengduan Mountains, and East Himalaya regions.

RESULTS

Our results revealed that the Sino-Himalayan flora developed from lowland biomes and was predominantly characterized by tropical floristic elements before the collision between the Indian subcontinent and Eurasia during the Early Cenozoic. Subsequently, from the Late Eocene onwards, the uplifts of the Himalaya and Hengduan Mountains transformed the Sino-Himalayan region into a wet and cold plateau, on which harsh and diverse ecological conditions forced the rapid evolution of local angiosperms, giving birth to characteristic taxa adapted to the high altitudes and cold habitat. The percentage of temperate floristic elements increased and exceeded that of tropical floristic elements by the Late Miocene.

CONCLUSIONS

The Sino-Himalayan flora underwent four significant formation periods and experienced a considerable increase in endemic genera and species in the Miocene, which remain crucial to the present-day patterns of plant diversity. Our findings support the view that the Sino-Himalayan flora is relatively young but has ancient origins. The three major shifts in the divergence of genera and species during the four formation periods were primarily influenced by the uplifts of the Himalaya and Hengduan Mountains and the onset and intensification of the Asian monsoon system. Additionally, the temporal patterns of floristic elements differed among the three floristic regions of the Sino-Himalaya, indicating that the uplift of the Himalaya and surrounding areas was asynchronous. Compared to the Yunnan Plateau region, the East Himalaya and Hengduan Mountains experienced more recent and drastic uplifts, resulting in highly intricate topography with diverse habitats that promoted the rapid radiation of endemic genera and species in these regions.

Himalayan upliftment and Shiwalik succession act as a cradle for divergence in Bengal monitor lizard Varanus bengalensis (Reptilia: Varanidae) in India

The Himalayan foothills and associated environment are well-known for driving the rapid diversification of many species and the formation of biodiversity hotspots. The effects of environmental change since the Miocene have accelerated species diversification, and hence are useful for studying population genetic structure, and evolutionary relationships via genetic approaches. To date, the effects of climatic fluctuations on the biogeography of large-bodied lizards have not been assessed comprehensively. Herein, we examine the diversification of Varanus bengalensis, focusing on its genetic structure to provide insights into how landscape structure and climatic fluctuations have shaped species differentiation. We confirm the existence of two distinct lineages within V. bengalensis distributed across the Himalayan foothills and the remainder of mainland India. Divergence analyses revealed the split between the Himalayan foothills and the remainder of the mainland lineages of V. bengalensis in the mid-Pliocene ~3.06 Ma, potentially as a consequence of the Siwalik broadening and climatic fluctuations across the Himalayan foothills. The results suggest recognition of a new lineage of V. bengalensis from the Himalayan foothills as a distinctive evolutionarily significant unit.

Historical development of karst evergreen broadleaved forests in East Asia has shaped the evolution of a hemiparasitic genus Brandisia (Orobanchaceae)

Brandisia is a shrubby genus of about eight species distributed basically in East Asian evergreen broadleaved forests (EBLFs), with distribution centers in the karst regions of Yunnan, Guizhou, and Guangxi in southwestern China. Based on the hemiparasitic and more or less liana habits of this genus, we hypothesized that its evolution and distribution were shaped by the development of EBLFs there. To test our hypothesis, the most comprehensive phylogenies of Brandisia hitherto were constructed based on plastome and nuclear loci (nrDNA, PHYA and PHYB); then divergence time and ancestral areas were inferred using the combined nuclear loci dataset. Phylogenetic analyses reconfirmed that Brandisia is a member of Orobanchaceae, with unstable placements caused by nuclear-plastid incongruences. Within Brandisia, three major clades were well supported, corresponding to the three subgenera based on morphology. Brandisia was inferred to have originated in the early Oligocene (32.69 Mya) in the Eastern Himalayas-SW China, followed by diversification in the early Miocene (19.45 Mya) in karst EBLFs. The differentiation dates of Brandisia were consistent with the origin of keystone species of EBLFs in this region (e.g., Fagaceae, Lauraceae, Theaceae, and Magnoliaceae) and the colonization of other characteristic groups (e.g., Gesneriaceae and Mahonia). These findings indicate that the distribution and evolution of Brandisia were facilitated by the rise of the karst EBLFs in East Asia. In addition, the woody and parasitic habits, and pollination characteristics of Brandisia may also be the important factors affecting its speciation and dispersal.

Evolutionary history of the Arctic flora

The Arctic tundra is a relatively young and new type of biome and is especially sensitive to the impacts of global warming. However, little is known about how the Arctic flora was shaped over time. Here we investigate the origin and evolutionary dynamics of the Arctic flora by sampling 32 angiosperm clades that together encompass 3626 species. We show that dispersal into the Arctic and in situ diversification within the Arctic have similar trends through time, initiating at approximately 10-9 Ma, increasing sharply around 2.6 Ma, and peaking around 1.0-0.7 Ma. Additionally, we discover the existence of a long-term dispersal corridor between the Arctic and western North America. Our results suggest that the initiation and diversification of the Arctic flora might have been jointly driven by progressive landscape and climate changes and sea-level fluctuations since the early Late Miocene. These findings have important conservation implications given rapidly changing climate conditions in the Arctic.

Upward and outward growth of north-central Tibet: Mechanisms that build high-elevation, low-relief plateaus

Large orogenic plateaus, such as the Tibetan Plateau, are characterized by high-elevation, low-relief topography, in contrast to the rugged terrains of narrower mountain belts. A key question is how low-elevation hinterland basins, characteristic of broad regions of shortening, were raised while regional relief was flattened. This study uses the Hoh Xil Basin in north-central Tibet as an analogue for late-stage orogenic plateau formation. The precipitation temperatures of lacustrine carbonates deposited between ~19 and ~12 million years ago record an early to middle Miocene phase of surface uplift of 1.0 ± 0.7 km. The results of this study demonstrate the contribution of sub-surface geodynamic processes in driving regional surface uplift and redistribution of crustal material to flatten plateau surfaces during the late stage of orogenic plateau formation.

Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation

The Tibetan Plateau and adjacent mountain regions (TP; including the Tibetan Plateau, Himalaya, Hengduan Mountains and Mountains of Central Asia) harbor great biodiversity, some lineages on which may have undergone rapid radiations. However, only a few studies have investigated the evolutionary pattern of such diversification in depth using genomic data. In this study, we reconstructed a robust phylogeny backbone of Rhodiola, a lineage that may have undergone rapid radiation in the TP, using Genotyping-by-sequencing data, and conducted a series of gene flow and diversification analyses. The concatenation and coalescent-based methods yield similar tree topologies, and five well-supported clades were revealed. Potential gene flow and introgression events were detected, both between species from different major clades and closely related species, suggesting pervasive hybridization and introgression. An initial rapid and later slowdown of the diversification rate was revealed, indicating niche filling. Molecular dating and correlation analyses showed that the uplift of TP and global cooling in the mid-Miocene might have played an important role in promoting the rapid radiation of Rhodiola. Our work demonstrates that gene flow and introgression might be an important contributor to rapid radiation possibly by quickly reassembling old genetic variation into new combinations.

Adaptive evolution characteristics of mitochondrial genomes in genus Aparapotamon (Brachyura, Potamidae) of freshwater crabs

BACKGROUND

Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes.

RESULTS

A new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs.

CONCLUSIONS

Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.

Molecular phylogenetics and diversity of the Himalayan shrew ( Soriculus nigrescens Gray, 1842) (Eulipotyphla, Soricidae) in Southwest China

The Himalayan shrew, Soriculus nigrescens Gray, 1842, belongs to the monotypic genus Soriculus, which is distributed mainly in the Himalayan region. Previous authors have studied its classification based on morphological and molecular data. However, no comprehensive study of the diversity and phylogeny of this species has been performed. In this study, we investigated the molecular phylogeny, genetic diversity, and species divergence of S. nigrescens based on one mitochondrial gene and three nuclear genes. A total of 124 samples from 27 sites in Southwest China were analyzed. Our molecular phylogenetic analyses and species divergence reveal non-monophyly of Soriculus, potentially representing two genera and three clades. Populations from Yunnan (Clade YN) represent the subspecies S. n. minors and should recover the full species status. Populations from Himalayas (Clade A) represent the species S. nigrescens, while populations from southeastern Nyenchen Tanglha Mountains and southern Himalayas (Clade B) represent a new cryptic and unnamed species. Species delimitation analyses and deep genetic distance analysis clearly support the species status of these three evolving clades. The putative new genus and cryptic species should be studied and identified in the future using a more extensive sampling combined with a comprehensive morphological and phylogenetic analysis.  

Why we should be looking for longitudinal patterns in biodiversity

Our understanding of global diversity patterns relies overwhelmingly on ecological and evolutionary correlates of latitude, and largely ignores longitude. However, the two major explanations of biodiversity patterns – energy and stability – are confounded across latitudes, and longitude offers potential solutions. Recent literature shows that the global biogeography of the Cenozoic world is structured by longitudinal barriers. In a few well-studied regions, such as South Africa’s Cape, the Himalayas and the Amazon-Andes continuum, there are strong longitudinal gradients in biodiversity. Often, such gradients occur where high and low past climatic velocities are juxtaposed, and there is clear evidence of higher biodiversity at the climatically-stable end. Understanding longitudinal biodiversity variations more widely can offer new insights towards biodiversity conservation in the face of anthropogenic climatic change.

Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia

Asia's rich species diversity has been linked to its Cenozoic geodiversity, including active mountain building and dramatic climatic changes. However, prior studies on the diversification and assembly of Asian faunas have been derived mainly from analyses at taxonomic or geographic scales too limited to offer a comprehensive view of this complex region's biotic evolution. Here, using the class Mammalia, we built historical biogeographic models drawn on phylogenies of 1,543 species occurring across Asia to investigate how and when the mammal diversity in Asian regions and mountain hotspots was assembled. We explore the roles of in situ speciation, colonization, and vicariance and geoclimatic events to explain the buildup of Asia's regional mammal diversity through time. We found that southern Asia has served as the main cradle of Asia's mammal diversity. Present-day species richness in other regions is mainly derived from colonization, but by the Miocene, in situ speciation increased in importance. The high biodiversity present in the mountain hotspots (Himalayas and Hengduan) that flank the Qinghai-Tibetan plateau is a product of high colonization instead of in situ speciation, making them important centers of lineage accumulation. Overall, Neogene was marked by great diversification and migrations across Asia and surrounding continents but Paleogene environments already hosted rich mammal assemblages. Our study revealed that synchronous diversification bursts and biotic turnovers are temporally associated with tectonic events (mountain building, continental collisions) and drastic reorganization of climate (aridification of Asian interior, intensification of Asian monsoons, sea retreat) that took place throughout the Cenozoic in Asia.

Monsoon intensification in East Asia triggered the evolution of its flora

INTRODUCTION

East Asia (EA), which falls within the region of the Asian monsoon that is composed of the East Asia monsoon (EAM) and the Indian monsoon (IM), is known for its high species diversity and endemism. This has been attributed to extreme physiographical heterogeneity in conjunction with climate and sea-level changes during the Pleistocene, this hypothesis has been widely proven by phylogeographic studies. Recently, dated phylogenies have indicated that the origins (stem age) of the flora occurred after the Oligocene-Miocene boundary and are related to the establishment of the EAM.

METHODS

Hence, this study further examined whether the strengthening of the monsoons triggered floral evolution via a meta-analysis of the tempo-spatial pattern of evolutionary radiation dates (crown ages) of 101 endemic seed plant genera.

RESULTS

Taxonomic diversification began during the late Eocene, whereas the accumulated number of diversifications did not significantly accelerate until the late Miocene. The distribution of the weighted mean and the average divergence times in the EAM, IM, or transitional regions all fall within the mid-late Miocene. Fossils of the Tertiary relict genera are mostly and widely distributed outside EA and only half of the earliest fossils in the EA region are not older than Miocene, while their divergence times are mostly after the late Miocene. The pattern of divergence time of monotypic and polytypic taxa suggest the climatic changes after the late Pliocene exert more influence on monotypic taxa.

DISCUSSION

The two key stages of floral evolution coincide with the intensifications of the EAM and IM, especially the summer monsoon which brings a humid climate. An integrated review of previous studies concerning flora, genus, and species levels further supports our suggestion that monsoon intensification in EA triggered the evolution of its flora.

The Effect of Environmental Factors on the Diversity of Crane Flies (Tipulidae) in Mountainous and Non-Mountainous Regions of the Qinghai-Tibet Plateau and Surrounding Areas

Tipulidae, one of the most diverse families of Diptera, is widely distributed in the world. The adults have weak flight ability, making it an ideal model for studying the formation of insect diversity. This study aims to explore the species diversity and endemism of Tipulidae in the Qinghai-Tibet Plateau and the surrounding areas, as well as analyze the relationships between the diversity pattern and 25 environmental factors in mountainous and non-mountainous regions. To this end, we collected 2589 datasets for the distribution of 1219 Tipulidae species, and found three areas with high diversities of Tipulidae around the QTP, including the Sikkim-Yadong area, Kamen River Basin, and Gongga Mountain. Further R, generalized additive model (GAM), and stepwise multiple regression analysis indicated that the richness and endemism of Tipulidae is mainly influenced by the warmest quarter precipitation and topographic heterogeneity in mountainous regions, but in non-mountainous regions, the richness is mostly affected by the precipitation seasonality, while there is no regularity in the relationship between endemism and environmental factors. In addition, the richness model in mountainous regions was in conformity with the results of GAM.

A distinctive Eocene Asian monsoon and modern biodiversity resulted from the rise of eastern Tibet

The uplift of eastern Tibet, Asian monsoon development and the evolution of globally significant Asian biodiversity are all linked, but in obscure ways. Sedimentology, geochronology, clumped isotope thermometry, and fossil leaf-derived numerical climate data from the Relu Basin, eastern Tibet, show at ∼50-45 Ma the basin was a hot (mean annual air temperature, MAAT, ∼27 °C) dry desert at a low-elevation of 0.6 ± 0.6 km. Rapid basin rise to 2.0 ± 0.9 km at 45-42 Ma and to 2.9 ± 0.9 km at 42-40 Ma, with MAATs of ∼20 and ∼16 °C, respectively, accompanied seasonally varying increased annual precipitation to > 1500 mm. From ∼39 to 34 Ma, the basin attained 3.5 ± 1.0 km, near its present-day elevation (∼3.7 km), and MAAT cooled to ∼6 °C. Numerically-modelled Asian monsoon strength increased significantly when this Eocene uplift of eastern Tibet was incorporated. The simulation/proxy congruence points to a distinctive Eocene Asian monsoon, quite unlike that seen today, in that it featured bimodal precipitation and a winter-wet regime, and this enhanced biodiversity modernisation across eastern Asia. The Paleogene biodiversity of Asia evolved under a continually modifying monsoon influence, with the modern Asian monsoon system being unique to the present and a product of a long gradual development in the context of an ever-changing Earth system.

Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae)

The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai-Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.

Comparative multi-locus assessment of modern Asian newts ( Cynops, Paramesotriton, and Pachytriton: Salamandridae) in southern China suggests a shared biogeographic history

Evolutionary biologists are always interested in deciphering the geographic context of diversification, therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region. Here, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asian-endemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222 samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding, mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern China. Those ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP). Particularly, the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those newts. However, despite differences in realized niches between lineages, there is no evidence for divergence of fundamental niches. Preservation of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of speciation. Based on those results, we advocate a multi-pronged protection strategy for newts in the three genera.

Phylogeographic analyses of an epiphytic foliose lichen show multiple dispersal events westward from the Hengduan Mountains of Yunnan into the Himalayas

Lobaria pindarensis is an endemic species of the Himalayas and the Hengduan Mountains. Little information is available on the phylogeography genetics and colonization history of this species or how its distribution patterns changed in response to the orographic history of the Himalayas and Hengduan Mountains. Based on samples covering a major part of the species' distribution range, we used 443 newly generated sequences of nine loci for molecular coalescent analyses in order to reconstruct the evolutionary history of L. pindarensis, and to reconstruct the species' ancestral phylogeographic distributions using Bayesian binary MCMC analyses. The results suggest that current populations originated from the Yunnan region of the Hengduan Mountains in the middle Pliocene, and that the Himalayas of Bhutan were colonized by a lineage that diverged from Yunnan ca. 2.72 Ma. The analysis additionally indicates that the Nepal and Xizang areas of the Himalayas were colonized from Yunnan as well, and that there was later a second dispersal event from Yunnan to Bhutan. We conclude that the change in climate and habitat related to the continuous uplift of the Himalayas and the Hengduan Mountains in the late Pliocene and middle Pleistocene influenced the geographic distribution pattern of L. pindarensis.

Fingerprints of climatic changes through the late Cenozoic in southern Asian flora: Magnolia section Michelia (Magnoliaceae)

BACKGROUND AND AIMS

Ongoing global warming is a challenge for humankind. A series of drastic climatic changes have been proven to have occurred throughout the Cenozoic based on a variety of geological evidence, which helps to better understand our planet's future climate. Notably, extant biomes have recorded drastic environmental shifts. The climate in southern Asia, which hosts high biodiversity, is deeply impacted by the Asian monsoon. The origins and evolutionary dynamics of biomes occurring between the tropics and sub-tropics in southern Asia have probably been deeply impacted by climatic changes; however, these aspects remain poorly studied. We tested whether the evolutionary dynamics of the above biomes have recorded the drastic, late Cenozoic environmental shifts, by focusing on Magnolia section Michelia of the family Magnoliaceae.

METHODS

We established a fine time-calibrated phylogeny of M. section Michelia based on complete plastid genomes and inferred its ancestral ranges. Finally, we estimated the evolutionary dynamics of this section through time, determining its diversification rate and the dispersal events that occurred between tropical and sub-tropical areas.

KEY RESULTS

The tropical origin of M. section Michelia was dated to the late Oligocene; however, the diversification of its core group (i.e. M. section Michelia subsection Michelia) has occurred mainly from the late Miocene onward. Two key evolutionary shifts (dated approx. 8 and approx. 3 million years ago, respectively) were identified, each of them probably in response to drastic climatic changes.

CONCLUSION

Here, we inferred the underlying evolutionary dynamics of biomes in southern Asia, which probably reflect late Cenozoic climatic changes. The occurrence of modern Asian monsoons was probably fundamental for the origin of M. section Michelia; moreover, the occurrence of asymmetric dispersal events between the tropics and sub-tropics hint at an adaptation strategy of M. section Michelia to global cooling, in agreement with the tropical conservatism hypothesis.

Rapid Eocene diversification of spiny plants in subtropical woodlands of central Tibet

Spinescence is an important functional trait possessed by many plant species for physical defence against mammalian herbivores. The development of spinescence must have been closely associated with both biotic and abiotic factors in the geological past, but knowledge of spinescence evolution suffers from a dearth of fossil records, with most studies focusing on spatial patterns and spinescence-herbivore interactions in modern ecosystems. Numerous well-preserved Eocene (~39 Ma) plant fossils exhibiting seven different spine morphologies discovered recently in the central Tibetan Plateau, combined with molecular phylogenetic character reconstruction, point not only to the presence of a diversity of spiny plants in Eocene central Tibet but a rapid diversification of spiny plants in Eurasia around that time. These spiny plants occupied an open woodland landscape, indicated by numerous megafossils and grass phytoliths found in the same deposits, as well as numerical climate and vegetation modelling. Our study shows that regional aridification and expansion of herbivorous mammals may have driven the diversification of functional spinescence in central Tibetan woodlands, ~24 million years earlier than similar transformations in Africa.

Spines are an important physical defense for many plant species. Here, the authors describe seven different spine morphologies from the Eocene of central Tibet associated with regional aridification and expansion of herbivorous mammals.

Himalayan orogeny and monsoon intensification explain species diversification in an endemic ginger (Hedychium: Zingiberaceae) from the Indo-Malayan Realm

The Indo-Malayan Realm is a biogeographic realm that extends from the Indian Subcontinent to the islands of Southeast Asia (Malay Archipelago). Despite being megadiverse, evolutionary hypotheses explaining taxonomic diversity in this region have been rare. Here, we investigate the role of geoclimatic events such as Himalayan orogeny and monsoon intensification in the diversification of the ginger-lilies (Hedychium J.Koenig: Zingiberaceae). We first built a comprehensive, time-calibrated phylogeny of Hedychium with 75% taxonomic and geographic sampling. We found that Hedychium is a very young lineage that originated in Northern Indo-Burma, in the Late Miocene (c. 10.6 Ma). This was followed by a late Neogene and early Quaternary diversification, with multiple dispersal events to Southern Indo-Burma, Himalayas, Peninsular India, and the Malay Archipelago. The most speciose clade IV i.e., the predominantly Indo-Burmese clade also showed a higher diversification rate, suggesting its recent rapid radiation. Our divergence dating and GeoHiSSE results demonstrate that the diversification of Hedychium was shaped by both the intensifications in the Himalayan uplift as well as the Asian monsoon. Ancestral character-state reconstructions identified the occurrence of vegetative dormancy in both clades I and II, whereas the strictly epiphytic growth behavior, island dwarfism, lack of dormancy, and a distinct environmental niche were observed only in the predominantly island clade i.e., clade III. Finally, we show that the occurrence of epiphytism in clade III corresponds with submergence due to sea-level changes, suggesting it to be an adaptive trait. Our study highlights the role of recent geoclimatic events and environmental factors in the diversification of plants within the Indo-Malayan Realm and the need for collaborative work to understand biogeographic patterns within this understudied region. This study opens new perspectives for future biogeographic studies in this region and provides a framework to explain the taxonomic hyperdiversity of the Indo-Malayan Realm.

Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) sensu lato (sl), comprising the platform, the Himalaya and the Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because of geographic isolation. However, gene flow has been widely detected during the speciation processes of all groups examined, suggesting that natural selection may have also played an important role during species divergence in this region. In addition, natural hybrids have been recovered in almost all species-rich genera. This suggests that numerous species in this region are still 'on the speciation pathway to complete reproductive isolation (RI)'. Such hybrids could directly develop into new species through hybrid polyploidization and homoploid hybrid speciation (HHS). HHS may take place more easily than previously thought through alternate inheritance of alleles of parents at multiple RI loci. Therefore, isolation, selection and hybridization could together have promoted species diversification of numerous plant genera on the QTP sl. We emphasize the need for identification and functional analysis of alleles of major genes for speciation, and especially encourage investigations of parallel adaptive divergence causing RI across different lineages within similar but specific habitats in this region.

Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.

Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the Scrophularia incisa complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China

Numerous temperate plants and animals on the Qinghai-Tibet Plateau (QTP) are hypothesized to have differentiated due to vicariant allopatric speciation associated with the geologic uplifts. However, this hypothesis has rarely been tested through a phylogeographic study of relative species in a broader geographic context, including the QTP, Tianshan Mountains, Mongolian Plateau, and surrounding regions. To understand the speciation and diversification process of plants across this wide area, phylogeographic analysis were examined from Scrophularia incisa and two other closely relative species comprising S. kiriloviana and S. dentata. Thirty-two populations of the three close relatives were genotyped using chloroplast DNA fragments and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and species distribution modelings, as well as niche identity tests. Our chloroplast DNA (cpDNA) phylogeny showed that this monophyletic group of desert and steppe semi-shrub is derived from a Middle Pliocene ancestor of the Central Asia. Lineages in Central Asia vs. China diverged through climate/tectonic-induced vicariance during Middle Pliocene. Genetic and ENM data in conjunction with niche differentiation analyses support that the divergence of S. incisa, S. dentata and S. kiriloviana in China lineage proceeded through allopatric speciation, might triggered by early Pleistocene climate change of increase of aridification and enlargement of deserts, while subsequent climate-induced cycles of range contractions/expansions enhanced the geographical isolation and habit fragmentation of these taxa. These findings highlight the importance of the Plio-Pleistocene climate change in shaping genetic diversity and driving speciation in temperate steppes and deserts of Northwestern China.

Phylogeography of Iris loczyi (Iridaceae) in Qinghai-Tibet Plateau revealed by chloroplast DNA and microsatellite markers

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.

Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau

Genus Comastoma (subt. Swertiinae, Gentianaceae) contains species, such as "Zangyinchen," that are important herbs in Tibetan medicine. The phylogenetic relationship of this within Gentianaceae and the circumscriptions of its species have long been controversial with conflicting morphological and molecular data reported. Here, we used whole chloroplast genome sequences for Comastoma species and related taxa to reconstruct their phylogeny and clarify their taxonomic relationships. The results revealed that the length of all plastome sequenced varied from 149 to 151 kb and have high similarity in structure and gene content. Phylogenomic analysis showed that Comastoma is a monophyletic group, closely related to the genus Lomatogonium. The divergence time estimation showed that Gentianaceae diverged at about 21.81 Ma, while the split of Comastoma occurred at 7.70 Ma. However, the results suggested the crown age of species formation in this genus is after 4.19 Ma. Our results suggest that QTP uplift, the alternation of Quaternary glaciation and interglaciation, and monsoon changes might have acted as drivers of speciation in Comastoma.

Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification

The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. The Himalayan region is a relatively small area but with exceptional diversity and endemism. One common hypothesis to explain the rich montane diversity is uplift-driven diversification-that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We test this hypothesis in the Himalayan region using amphibians and reptiles, two environmentally sensitive vertebrate groups. In addition, analysis of diversification of the herpetofauna provides an independent source of information to test competing geological hypotheses of Himalayan orogenesis. We conclude that the origins of the Himalayan herpetofauna date to the early Paleocene, but that diversification of most groups was concentrated in the Miocene. There was an increase in both rates and modes of diversification during the early to middle Miocene, together with regional interchange (dispersal) between the Himalaya and adjacent regions. Our analyses support a recently proposed stepwise geological model of Himalayan uplift beginning in the Paleocene, with a subsequent rapid increase of uplifting during the Miocene, finally giving rise to the intensification of the modern South Asian Monsoon.

Speciation along the elevation gradient: Divergence of Roscoea species within the south slope of the Himalayas

The Himalayas with dramatic elevation gradient is one of the global biodiversity hotspots. Although origin of biodiversity of the Himalayas is of great concern, the speciation process within the Himalayas is poorly known. Roscoea within the Himalayas serve as a good model system to test the speciation process along an elevation gradient. 32,375 unlinked SNPs were used to reconstruct phylogenetic relationships and introgression analyses in D-statistics and Fastsimicoal2. Species distribution modeling (SDM) was used to simulate habitat shift of Roscoea species during climate changes. Phylogeny suggested that the speciation order, except R. capitata, was from highland to lowland. D-statistics analyses suggested significant bidirectional ancient introgression between elevation-neighboring clades but no introgression between R. capitata and othern clades and no introgression among extant species. Fastsimicoal2 suggested interspecific introgressions were asymmetric. SDM predicted that habitats of Roscoea shifted to low elevation during cooling age. These results suggested that the sudden uplift of the Himalayas likely promoted speciation by vicariance, and climate cooling drove species divergence towards lower elevation. This study provides explanations for the origin of biodiversity within the Himalayas, and an insight to understand speciation along elevation in the mountainous regions.

Phylogeny, origin, and dispersal of Dubyaea (Asteraceae) based on Hyb-Seq data

Dubyaea DC. is a small genus of Asteraceae that is almost exclusively endemic to the Pan-Himalayan region. Within Dubyaea, phylogenetic relationships remain poorly understood. Here, our well-supported phylogeny based on Hyb-Seq data shows that all samples of Dubyaea in this study belong to a monophyletic group, which is sister to the clade of Soroseris, Syncalathium, and Nabalus. Dubyaea (s. str.) can be divided into three major clades, which are supported by flower color as well as morphological features of the stems and basal leaves. Based on our phylogenetic results, we performed biogeographic analyses and inferred that Dubyaea arose in the late Miocene in Hengduan Mountains and its eastern areas. Following its evolutionary origin, Dubyaea underwent diversification in situ as well as spread to the Himalayas.

Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives

Mountain ecosystems support a significant one-third of all terrestrial biodiversity, but our understanding of the spatiotemporal maintenance of this high biodiversity remains poor, or at best controversial. The Himalaya hosts a complex mountain ecosystem with high topographic and climatic heterogeneity and harbors one of the world's richest floras. The high species endemism, together with increasing anthropogenic threats, has qualified the Himalaya as one of the most significant global biodiversity hotspots. The topographic and climatic complexity of the Himalaya makes it an ideal natural laboratory for studying the mechanisms of floral exchange, diversification, and spatiotemporal distributions. Here, we review literature pertaining to the Himalaya in order to generate a concise synthesis of the origin, distribution, and climate change responses of the Himalayan flora. We found that the Himalaya supports a rich biodiversity and that the Hengduan Mountains supplied the majority of the Himalayan floral elements, which subsequently diversified from the late Miocene onward, to create today's relatively high endemicity in the Himalaya. Further, we uncover links between this Miocene diversification and the joint effect of geological and climatic upheavals in the Himalaya. There is marked variance regarding species dispersal, elevational gradients, and impact of climate change among plant species in the Himalaya, and our review highlights some of the general trends and recent advances on these aspects. Finally, we provide some recommendations for conservation planning and future research. Our work could be useful in guiding future research in this important ecosystem and will also provide new insights into the maintenance mechanisms underpinning other mountain systems.

Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

BACKGROUND

The Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet.

METHODS

We obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests.

RESULTS

Consistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau.

Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae)

Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.

Southeast Asia as One of World’s Primary Sources of Biotic Recolonization Following Anthropocene Extinctions

The plight of Southeast Asia’s animals, plants and ecosystems in the face of unsustainable exploitation and habitat destruction has been illustrated in several recent studies, despite often falling outside the global discourse on global conservation priorities. Here, we collate biogeographic and phylogenetic information to argue that this beleaguered region is one of world’s primary macrorefugia, and possibly its best chance of regaining its natural biodiversity distribution patterns after the current Anthropocene upheaval. The region uniquely combines top diversity values in (a) ancient lineage diversity and (b) cosmopolitan lineage diversity, suggesting that it has acted in the past as a biodiversity museum and source of global colonization. This is at least partly due to the interplay between latitudinal diversity gradients and continental connectivity patterns. However, the peak values in South China/North Indochina for cosmopolitan tetrapods and their sister lineages suggest that a key feature is also the availability of diverse climatic conditions. In particular, the north-south orientation of the mountain ranges here has allowed for rapid recolonization within the region following past climatic changes, resulting in high survival values and overall exceptional relict lineage diversity. From this starting point, global colonization occurred on multiple occasions. It is hoped that, with urgent action, the region can once again fulfill this function.

Orographic evolution of northern Tibet shaped vegetation and plant diversity in eastern Asia

The growth of the Tibetan Plateau throughout the past 66 million years has profoundly affected the Asian climate, but how this unparalleled orogenesis might have driven vegetation and plant diversity changes in eastern Asia is poorly understood. We approach this question by integrating modeling results and fossil data. We show that growth of north and northeastern Tibet affects vegetation and, crucially, plant diversity in eastern Asia by altering the monsoon system. This northern Tibetan orographic change induces a precipitation increase, especially in the dry (winter) season, resulting in a transition from deciduous broadleaf vegetation to evergreen broadleaf vegetation and plant diversity increases across southeastern Asia. Further quantifying the complexity of Tibetan orographic change is critical for understanding the finer details of Asian vegetation and plant diversity evolution.

Why 'the uplift of the Tibetan Plateau' is a myth

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.

Diversification in Qinghai-Tibet Plateau: Orchidinae (Orchidaceae) clades exhibiting pre-adaptations play critical role

We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species-richness of Orchidinae arose through a combination of in situ diversification, colonisation, and local recruitment. There are multiple origins of species-richness of Orchidinae in the QTP, and pre-adaptations in clades from North Temperate and alpine regions were crucial for in situ diversification. The geographic analysis identified 29 dispersals from Asia, Africa and Europe into the QTP and 15 dispersals out. Most endemic species of Orchidinae evolved within the past six million years.

A Middle Eocene lowland humid subtropical "Shangri-La" ecosystem in central Tibet

Tibet's ancient topography and its role in climatic and biotic evolution remain speculative due to a paucity of quantitative surface-height measurements through time and space, and sparse fossil records. However, newly discovered fossils from a present elevation of ∼4,850 m in central Tibet improve substantially our knowledge of the ancient Tibetan environment. The 70 plant fossil taxa so far recovered include the first occurrences of several modern Asian lineages and represent a Middle Eocene (∼47 Mya) humid subtropical ecosystem. The fossils not only record the diverse composition of the ancient Tibetan biota, but also allow us to constrain the Middle Eocene land surface height in central Tibet to ∼1,500 ± 900 m, and quantify the prevailing thermal and hydrological regime. This "Shangri-La"-like ecosystem experienced monsoon seasonality with a mean annual temperature of ∼19 °C, and frosts were rare. It contained few Gondwanan taxa, yet was compositionally similar to contemporaneous floras in both North America and Europe. Our discovery quantifies a key part of Tibetan Paleogene topography and climate, and highlights the importance of Tibet in regard to the origin of modern Asian plant species and the evolution of global biodiversity.

Cenozoic evolution of the steppe-desert biome in Central Asia

The origins and development of the arid and highly seasonal steppe-desert biome in Central Asia, the largest of its kind in the world, remain largely unconstrained by existing records. It is unclear how Cenozoic climatic, geological, and biological forces, acting at diverse spatial and temporal scales, shaped Central Asian ecosystems through time. Our synthesis shows that the Central Asian steppe-desert has existed since at least Eocene times but experienced no less than two regime shifts, one at the Eocene-Oligocene Transition and one in the mid-Miocene. These shifts separated three successive "stable states," each characterized by unique floral and faunal structures. Past responses to disturbance in the Asian steppe-desert imply that modern ecosystems are unlikely to recover their present structures and diversity if forced into a new regime. This is of concern for Asian steppes today, which are being modified for human use and lost to desertification at unprecedented rates.

Cenozoic topography, monsoons and biodiversity conservation within the Tibetan Region: An evolving story

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.

Asian monsoon shaped the pattern of woody dicotyledon richness in humid regions of China

Understanding how geographical patterns of plant richness are established is a key scientific question in ecology and biogeography. Climate factors, such as environmental energy, water availability, and rainfall seasonality, have been widely proposed to account for geographical patterns of plant richness at large scales. Using a compiled distribution data set of 3166 native woody dicotyledons across 732 calibration grids at the county level in humid regions of China, we explored the geographical pattern of woody dicotyledon richness and its relationship to climatic variations, especially the Asian monsoonal climate. We found that species richness decreases with increasing latitude. Our study indicates that water availability (particularly mean annual precipitation, MAP) is the major abiotic factor in determining large-scale distribution patterns of species richness. Moreover, the seasonality of rainfall variables under the Asian monsoon climate largely contributes to species richness, because species richness correlates more significantly with precipitation during the three driest consecutive months (P3DRY) than precipitation during the three wettest consecutive months (P3WET). Therefore, we conclude that woody dicotyledon richness in humid regions of China is mainly affected by the Asian winter monsoon.

Karyomorphology of three endemic plants (Brassicaceae: Euclidieae and Arabideae) from the Qinghai-Tibet Plateau and its significance

In the paper, chromosome number and karyotype of three endemic genera from China are reported for the first time. Our results show that Anzhengxia yechengnica has a karyotype formula 2n = 2x = 14 = 6 m + 8sm and belongs to Stebbins-3A; Shangrilaia nana karyotype formula is 2n = 2x = 14 = 10 m + 4sm (2sat) and belongs to Stebbins-1A; Baimashania pulvinata karyotype formula is 2n = 2x = 16 = 12 m (2sat) + 4sm and belongs to Stebbins-1A. Anzhengxia and Shangrilaia are monospecific genera belonging to tribe Euclidieae and both have a basic chromosome x = 7. Baimashania, which belongs to tribe Arabideae, has two species which have a basic chromosome x = 8. The implications of these cytological data are compared with morphological support and the implications for each tribe are discussed. We also summarize chromosomal number variation and its systematic implications of two tribes from the Qinghai-Tibet Plateau.

Mountains as a Global Heritage: Arguments for Conserving the Natural Diversity of Mountain Regions

This concise review posits the urgent need for conserving the natural diversity of mountain environments by envisioning mountains as a global natural heritage. Mountains are recognized as cradles of biodiversity and for their important ecosystem services. Mountains also constitute the second most popular outdoor destination category at the global level after islands and beaches. However, in the current age of accelerating global environmental change, mountain systems face unprecedented change in their ecological characteristics, and consequent effects will extend to the millions who depend directly on ecosystem services from mountains. Moreover, growing tourism is putting fragile mountain ecosystems under increasing stress. This situation requires scientists and mountain area management stakeholders to come together in order to protect mountains as a global heritage. By underlining the salient natural diversity characteristics of mountains and their relevance for understanding global environmental change, this critical review argues that it is important to appreciate both biotic and abiotic diversity features of mountains in order to create a notion of mountains as a shared heritage for humanity. Accordingly, the development of soft infrastructure that can communicate the essence of mountain destinations and a committed network of scientists and tourism scholars working together at the global level are required for safeguarding this shared heritage.

Asclepiadospermum gen. nov., the earliest fossil record of Asclepiadoideae (Apocynaceae) from the early Eocene of central Qinghai-Tibetan Plateau, and its biogeographic implications

PREMISE

Apocynaceae is common in the fossil record, especially as seed remains from the Neogene of Europe and North America, but rare in Asia. Intrafamilial assignment is difficult due to the lack of diagnostic characters, and new fossil and modern data are needed to understand the paleobiogeography of this group.

METHODS

We studied three Apocynaceae seed impressions from the Lower Eocene Niubao Formation, Jianglang village, Bangor County, central Qinghai-Tibetan Plateau. Morphological data from living and fossil species were phylogenetically mapped to enable systematic assignment.

RESULTS

We describe a new genus, Asclepiadospermum gen. nov., and two new species, A. marginatum sp. nov. and A. ellipticum sp. nov. These species are characterized by an elliptical seed, a margin surrounding the central part of the seed, and polygonal, irregular, and small epidermal cells, and differ mainly in terms of the size of the margin and the shape of the apex. All these characters indicate that this new genus belongs to the subfamily Asclepiadoideae (Apocynaceae).

CONCLUSIONS

These fossils represent the earliest fossil seed records of Asclepiadoideae. Asclepiadospermum indicates a humid tropical to subtropical flora during the early Eocene in central Tibet. Moreover, our discoveries indicate a close floristic connection between Eurasia and Africa during the early Eocene, which expands our knowledge of the floristic linkage between Tibet and other regions at that time.

Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group

Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.