The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas

Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

Ancient orogenic and monsoon-driven assembly of the world's richest temperate alpine flora

Understanding how alpine biotas formed in response to historical environmental change may improve our ability to predict and mitigate the threats to alpine species posed by global warming. In the world's richest temperate alpine flora, that of the Tibet-Himalaya-Hengduan region, phylogenetic reconstructions of biome and geographic range evolution show that extant lineages emerged by the early Oligocene and diversified first in the Hengduan Mountains. By the early to middle Miocene, accelerated diversification and colonization of adjacent regions were likely driven jointly by mountain building and intensification of the Asian monsoon. The alpine flora of the Hengduan Mountains has continuously existed far longer than any other alpine flora on Earth and illustrates how modern biotas have been shaped by past geological and climatic events.

"Into and Out of" the Qinghai-Tibet Plateau and the Himalayas: Centers of origin and diversification across five clades of Eurasian montane and alpine passerine birds

Encompassing some of the major hotspots of biodiversity on Earth, large mountain systems have long held the attention of evolutionary biologists. The region of the Qinghai-Tibet Plateau (QTP) is considered a biogeographic source for multiple colonization events into adjacent areas including the northern Palearctic. The faunal exchange between the QTP and adjacent regions could thus represent a one-way street ("out of" the QTP). However, immigration into the QTP region has so far received only little attention, despite its potential to shape faunal and floral communities of the QTP. In this study, we investigated centers of origin and dispersal routes between the QTP, its forested margins and adjacent regions for five clades of alpine and montane birds of the passerine superfamily Passeroidea. We performed an ancestral area reconstruction using BioGeoBEARS and inferred a time-calibrated backbone phylogeny for 279 taxa of Passeroidea. The oldest endemic species of the QTP was dated to the early Miocene (ca. 20 Ma). Several additional QTP endemics evolved in the mid to late Miocene (12-7 Ma). The inferred centers of origin and diversification for some of our target clades matched the "out of Tibet hypothesis' or the "out of Himalayas hypothesis" for others they matched the "into Tibet hypothesis." Three radiations included multiple independent Pleistocene colonization events to regions as distant as the Western Palearctic and the Nearctic. We conclude that faunal exchange between the QTP and adjacent regions was bidirectional through time, and the QTP region has thus harbored both centers of diversification and centers of immigration.

The East Asian Winter Monsoon Acts as a Major Selective Factor in the Intraspecific Differentiation of Drought-Tolerant Nitraria tangutorum in Northwest China

The influence of Quaternary climate fluctuation on the geographical structure and genetic diversity of species distributed in the regions of the Qinghai–Tibet Plateau (QTP) has been well established. However, the underlying role of the East Asian monsoon system (EAMS) in shaping the genetic structure of the population and the demography of plants located in the arid northwest of China has not been explored. In the present study, Nitraria tangutorum, a drought-tolerant desert shrub that is distributed in the EAMS zone and has substantial ecological and economic value, was profiled to better understand the influence of EAMS evolution on its biogeographical patterns and demographic history. Thus, the phylogeographical structure and historical dynamics of this plant species were elucidated using its five chloroplast DNA (cpDNA) fragments. Hierarchical structure analysis revealed three distinct, divergent lineages: West, East-A, and East-B. The molecular dating was carried out using a Bayesian approach to estimate the time of intraspecies divergence. Notably, the eastern region, which included East-A and East-B lineages, was revealed to be the original center of distribution and was characterized by a high level of genetic diversity, with the intraspecific divergence time dated to be around 2.53 million years ago (Ma). These findings, combined with the data obtained by ecological niche modeling analysis, indicated that the East lineages have undergone population expansion and differentiation, which were closely correlated with the development of the EAMS, especially the East Asian winter monsoon (EAWM). The West lineage appears to have originated from the migration of N. tangutorum across the Hexi corridor at around 1.85 Ma, and subsequent colonization of the western region. These results suggest that the EAWM accelerated the population expansion of N. tangutorum and subsequent intraspecific differentiation. These findings collectively provide new information on the impact of the evolution of the EAMS on intraspecific diversification and population demography of drought-tolerant plant species in northwest China.

Miocene diversification of a golden-thread nanmu tree species (Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon

Understanding the role of climate changes and geography as drivers of population divergence and speciation is a long‐standing goal of evolutionary biology and can inform conservation. In this study, we used restriction site‐associated DNA sequencing (RAD‐seq) to evaluate genetic diversity, population structure, and infer demographic history of the endangered tree, Phoebe zhennan which is distributed around the Sichuan Basin. Genomic patterns revealed two distinct clusters, each largely confined to the West and East. Despite sympatry of the two genomic clusters at some sites, individuals show little or no evidence of genomic introgression. Demographic modeling supported an initial divergence time between the West and East lineages at ~15.08 Ma with further diversification within the West lineage at ~7.12 Ma. These times largely coincide with the two independent intensifications of the East Asian monsoon that were initiated during the middle (Langhian) and late Miocene (Messinian), respectively. These results suggest that the Miocene intensification phases of the East Asian monsoon played a pivotal role in shaping the current landscape‐level patterns of genetic diversity within P. zhennan, as has been found for the interspecific divergence of other subtropical Chinese plants. Based on isolation‐by‐distance and species distribution modeling, we hypothesize that P. zhennan followed a ring diversification which was facilitated by the Sichuan Basin acting as barrier to gene flow. In situ and ex situ conservation management plans should consider the results obtained in this study to help secure the future of this beautiful and culturally significant endangered tree.

Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks

Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.

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.

Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

The Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.

The Clinical and Molecular Characterization of Gastric Cancer Patients in Qinghai-Tibetan Plateau

Gastric cancer was the fifth most common malignancy and the third deadliest cancer (738,000 deaths in 2018) in the world. The analysis of its molecular characteristics has been complicated by histological and intratumor heterogeneity. Furthermore, the previous studies indicate that the incidence of gastric cancer shows wide geographical variation. As the largest and highest region in China, Qinghai-Tibetan Plateau (QTP) is one of the important global biodiversity hotspots. Here, to better understand the mechanism of gastric cancer and offer the targeted therapeutic strategies specially designed for patients in QTP, we collect tumor and blood samples from 30 primary gastric adenocarcinoma cancer patients at Qinghai Provincial People's Hospital. We discuss the clinical and molecular characteristics for these patients that have been ascribed to the unique features in this place, including high altitude (the average height above sea level is around 4,000 m), multi-ethnic groups, and the specific ways of life or habits (such as eating too much beef and mutton, have alcohol and cigarette problem, et al.). By comparing with the western gastric cancer patients collected from TCGA data portal, some unique characteristics for patients in QTP are suggested. They include high incidence in younger people, most of tumor are located in body, most of SNP are detected in chromosome 7, and the very different molecular atlas in minor ethnic groups and Han Chinese. These characteristics will provide the unprecedented opportunity to increase the efficacy for diagnosis and prognosis of gastric cancer in QTP. Furthermore, to suggest the targeted therapeutics specially designed for these 30 patients, an adapted kernel-based learning model and a compilation of pharmacogenomics data of 462 patient-derived tumor cells (PDCs) that illustrate the diverse genetic and molecular backgrounds of cancer patients, were introduced. In conclusion, our study offers a big opportunity to better understand the mechanism of gastric cancer in QTP and guide the optimal patient-tailored therapy for them.

Uncovering the role of a positive selection site of wax ester synthase/diacylglycerol acyltransferase in two closely related Stipa species in wax ester synthesis under drought stress

Natural selection drives local adaptations of species to biotic or abiotic environmental stresses. As a result, adaptive phenotypic divergence can evolve among related species living in different habitats. However, the genetic foundation of this divergence process remains largely unknown. Two closely related alpine grass species, Stipa capillacea and Stipa purpurea, are distributed in different rainfall regions of northern Tibet. Here, we analyzed the drought tolerance of these two closely related Stipa species, and found that S. purpurea was more resistance to drought stress than S. capillacea. To further understand the genetic diversity behind their adaptation to drought environments, a comprehensive gene repertoire was generated using PacBio isoform and Illumina RNA sequencing technologies. Bioinformatics analyses revealed that differential transcripts were mainly enriched in the wax synthetic pathway, and a threonine residue at position 239 of WSD1 was identified as having undergone positive selection in S. purpurea. Using heterologous expression in the Saccharomyces cerevisiae mutant H1246, site-directed mutagenesis studies demonstrated that a positive selection site results in changes to the wax esters profile. This difference may play an important role in S. purpurea in response to drought conditions, indicating that S. purpurea has evolved specific strategies involving its wax biosynthetic pathway as part of its long-term adaptation to the Qinghai-Tibet Plateau.

Population Genetic Structure and Demographic History of Primula fasciculata in Southwest China

Understanding the factors that drive the genetic structure of a species and its responses to past climatic changes is an important first step in modern population management. The response to the last glacial maximum (LGM) has been well studied, however, the effect of previous glaciation periods on plant demographic history is still not well studied. Here we investigated the population structure and demographic history of Primula fasciculata that widely occurs in the Hengduan Mountains and Qinghai-Tibetan Plateau. We obtained genomic data for 234 samples of the species using restriction site-associated DNA (RAD) sequencing and combined approximate Bayesian computation (ABC) and species distribution modeling (SDM) to evaluate the effects of multiple glaciation periods by testing several population divergence models and demographic scenarios. The analyses of population structure showed that P. fasciculata displays a striking population structure with six groups that could be identified genetically. Our ABC modeling suggested that the current groups diverged from ancestral populations located in the eastern Hengduan Mountains after the largest glaciation occurred in the region (~ 0.8-0.5 million years ago), which is consistent with the result of SDMs. Each current group has survived in different glacial refugia during the LGM and experienced expansions and/or bottlenecks since their divergence during or across the following Quaternary glacial cycles. Our study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes in alpine plant species with shallow population structure.

Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization

Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.

Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region

Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographical structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants, we used population genomic data of the Rheum palmatum complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection, to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the R. palmatum complex originated in the central Hengduan Mts and possibly in regions further east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the R. palmatum complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographical areas.

A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae)

BACKGROUND AND AIMS

A long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae.

METHODS

In total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration.

KEY RESULTS

A well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I-V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18-73.53 Mya).

CONCLUSIONS

This study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.

Molecular Phylogeography and Evolutionary History of the Endemic Species Corydalis hendersonii (Papaveraceae) on the Tibetan Plateau Inferred From Chloroplast DNA and ITS Sequence Variation

In response to past climatic changes, the species with different habits or adaptive traits likely have experienced very different evolutionary histories, especially for species that restricted to high mountain areas. In order to trace how Quaternary climatic oscillations affected range distributions and intraspecific divergence of such alpine plants on the Tibetan Plateau, here, we investigated maternally inherited chloroplast DNA (cpDNA) markers and biparentally inherited nuclear ribosomal internal transcribed spacer (ITS) DNA variations and aimed to explore the phylogeographic history of the endemic alpine species Corydalis hendersonii Hemsl. (Papaveraceae). We sequenced four cpDNA fragments (trnS-trnG, trnT-trnL, atpH-atpI, and psbE-petL) and also the nuclear (ITS) region in 368 individuals from 30 populations across the species' range. The network and phylogenetic analysis based on cpDNA variations identified 15 chlorotypes that cluster into three distinct clades. However, our nuclear DNA results demonstrated that there were four genetic/geographical groups within C. hendersonii. Some common and highly divergent cpDNA and ITS haplotypes were distributed in the populations of central and northeastern Tibetan Plateau, and the highest nucleotide diversity and genetic differentiation were detected in the central region. Demographic tests further indicated that the populations of southwestern and western Tibet may have experienced recent range expansion, which most likely occurred during the last glacial maximum (LGM) and continued its expansion after the beginning of the Holocene. These two different groups of this species may have derived from potential refugia that existed in the central and/or northeastern regions of Tibet during recent interglacial periods. In addition, our AMOVA analyses detected high genetic differentiation along with the whole sampling range. Also, distinct phylogeographic structures were detected among populations of C. hendersonii based on both of cpDNA and ITS variation. These findings shed new light on the importance of climatic oscillations during Quaternary and complex local topography as causes of intraspecific diversification and demographic changes within cold-tolerant herbs in the Tibetan Plateau biodiversity hotspot.

Dramatic impact of metric choice on biogeographical regionalization

For a quantitative biogeographical regionalization, the choice of an appropriate dissimilarity index to measure pairwise distances is crucial. Several different metrics have been used, but there is no specific study to test the impact of metric choice on biogeographical regionalization. We herein applied a hierarchical cluster analysis on the mean nearest taxon distance (MNTD) and the phylogenetic turnover component of the Sørensen dissimilarity index (pβ_sim) pairwise distances to generate two schemes of phylogenetic regionalization of the Chinese flora, and then evaluated the effect of metric choice. Floristic regionalization based on MNTD was influenced by richness differences, but regionalization based on pβ_sim can clearly reflect the evolutionary history of the Chinese flora. We provided a brief description of the five regions identified by pβ_sim, and the regionalization can help develop strategies to effectively conserve the taxa and floristic regions with different origins and evolutionary histories.

Population subdivision and hybridization in a species complex of Gentiana in the Qinghai-Tibetan Plateau

BACKGROUND AND AIMS

Hosting several global biodiversity hotspots, the region of the Qinghai-Tibetan Plateau (QTP) is exceptionally species-rich and harbours a remarkable level of endemism. Yet, despite a growing number of studies, factors fostering divergence, speciation and ultimately diversity remain poorly understood for QTP alpine plants. This is particularly the case for the role of hybridization. Here, we explored the evolutionary history of three closely related Gentiana endemic species, and tested whether our results supported the mountain geo-biodiversity hypothesis (MGH).

METHODS

We genotyped 69 populations across the QTP with one chloroplast marker and 12 nuclear microsatellite loci. We performed phylogeographical analysis, Bayesian clustering, approximate Bayesian computation and principal components analysis to explore their genetic relationship and evolutionary history. In addition, we modelled their distribution under different climates.

KEY RESULTS

Each species was composed of two geographically distinct clades, corresponding to the south-eastern and north-western parts of their distribution. Thus Gentiana veitchiorum and G. lawrencei var. farreri, which diverged recently, appear to have shared at least refugia in the past, from which their range expanded later on. Indeed, climatic niche modelling showed that both species went through continuous expansion from the Last Interglacial Maximum to the present day. Moreover, we have evidence of hybridization in the northwest clade of G. lawrencei var. farreri, which probably occurred in the refugium located on the plateau platform. Furthermore, phylogenetic and population genetic analyses suggested that G. dolichocalyx should be a geographically limited distinct species with low genetic differentiation from G. lawrencei var. farreri.

CONCLUSIONS

Climatic fluctuations in the region of the QTP have played an important role in shaping the current genetic structure of G. lawrencei var. farreri and G. veitchiorum. We argue that a species pump effect did occur prior to the Last Interglacial Maximum, thus lending support to the MGH. However, our results do depart from expectations as suggested in the MGH for more recent distribution range and hybridization dynamics.

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae)

The genus Amolops ("torrent frogs") is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of Amolops remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate species-level diversity within the genus Amolops throughout southern China and Southeast Asia, and infer evolutionary relationships among the species using mtDNA data (16S, COI, and ND2). Molecular analyses indicate nine unnamed species, mostly distributed in the Himalayas. We then utilized anchored hybrid enrichment to generate a dataset representing the major mitochondrial lineages to resolve phylogenetic relationships, biogeography, and pattern of species diversification. Our resulting phylogeny strongly supports the monophyly of four previously identified species groups (the A. ricketti, A. daiyunensis, A. hainanensis, and A. monticola groups), but paraphyly for the A. mantzorum and A. marmoratus groups, as previously defined. We erect one new species group, the A. viridimaculatus group, and recognize Dubois' (1992) subgenus Amo as the A. larutensis species group. Biogeographic analysis suggests that Amolops originated on the Indo-Burma/Thai-Malay Peninsula at the Eocene/Oligocene boundary, and dispersed outward, exemplifying a common pattern observed for the origin of Asian biodiversity. The early divergence within Amolops coincides with the Himalayan uplift and the lateral extrusion of Indochina at the Oligocene/Miocene boundary. Our results show that paleoclimatic and geomorphological events have profoundly influenced the patterns of lineage diversification within Amolops.

Phylogeography of the cicada Platypleura hilpa in subtropical and tropical East Asia based on mitochondrial and nuclear genes and microsatellite markers

Climate change and geographical events play key roles in driving population genetic structure of organisms, but different scenarios were suggested for species occurring in tropical and subtropical areas. We investigated the population genetic structure, diversity and demographic history of the cicada Platypleura hilpa which occurs in coastal areas of southern China and northeastern Indo-Burma, and analysed the potential impact of climate change and geological events on its evolutionary history. Our data imply that P. hilpa comprises five main lineages with nearly unique sets of haplotypes and distinct geographic distributions. A major split of the lineages occurred in the Pleistocene. Geographic distance and geomorphic barriers serve as the primary factors shaping the genetic population structure, and several climatic factors are associated with the divergence. The potential range during the Last Glacial Maximum has apparently increased in south China and the exposed South China Sea Shelf. The Pleistocene sea-level fluctuations had profound effects on the regional genetic structure. The Beibu Gulf represents a more important geographic barrier than the Qiongzhou Strait in blocking gene flow among populations. These results contribute to a better understanding of the pressure climatic change and geographical events impose on insects in coastal areas of East Asia.

Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies

Whole genome duplication (WGD) is commonly believed to play key roles in vertebrate evolution. However, nowadays polyploidy exists in a few fish, amphibian and reptile groups only, and seems to be an evolutionary dead end in vertebrates. We investigate the evolutionary significance of polyploidization in Cyprinidae-a fish family that contains more polyploid species than any other vertebrate group-with integrated biogeographic, phylogenetic and genomic analyses. First, polyploid species are found to be significantly frequent in areas of higher altitude and lower mean annual temperature compared with diploid species in Cyprinidae. Second, a polyploidy-related diversification rate shift is observed in Cyprinidae. This increased net diversification rate is only seen in three polyploid lineages, and other polyploid lineages have similar net diversification rate as well as diploid lineages in Cyprinidae. Interestingly, significant 'lag times' existed between polyploidization and radiation in Cyprinidae. Multiple polyploid lineages were established approximately 15 Ma through recurrent allopolyploidization events, but the net diversification rate did not start to increase until approximately 5 Ma-long after polyploidization events. Environmental changes associated with the continuous uplift of the Tibetan Plateau and climate change have probably promoted the initial establishment and subsequent radiation of polyploidy in Cyprinidae. Finally, the unique retention of duplicated genes in polyploid cyprinids adapted to harsh environments is found. Taken together, our results suggest that polyploidy in Cyprinidae is far more than an evolutionary dead end, but rather shows substantially adaptive potential. Polyploid cyprinids thus constitute an ideal model system for unveiling largely unexplored consequences of WGD in vertebrates, from genomic evolution to species diversification.

Phylogenetic relationships of the Chinese torrent frogs (Ranidae: Amolops) revealed by phylogenomic analyses of AFLP-Capture data

The torrent frog genus Amolops contains nearly sixty species distributed in swift mountain streams throughout southeast Asia. The taxonomy of this genus has proven complicated due to unstable morphological diagnostic characters. The relationships of Amolops species and species groups were not readily resolved with a small number of molecular markers. Here, we applied the novel AFLP-Capture approach and acquired two large datasets (242 anonymous nuclear sequences and the mitochondrial genome) from 70 Chinese Amolops samples to study their relationships. The phylogenies inferred from the nuclear data and the mitochondrial data were both robust and revealed a primary phylogenetic split between eastern and western Chinese Amolops species. The relationships of the six species groups were clarified. While the three species groups in east China (the A. ricketti, A. daiyunensis and A. hainanensis groups) were monophyletic, the three species groups in the west (the A. mantzorum, A. monticola and A. marmoratus groups) were not monophyletic, suggesting a need for further investigation and revision. The robust phylogenies also provided new insights into species relationships, especially for the A. mantzorum group, which has been difficult to resolve due to multiple speciation events occurring approximately 7-8 million years ago. The divergence times estimated with the nuclear data indicated that the ancestor of the Chinese Amolops appeared in the late Eocene or early Oligocene, and that speciation events in the Chinese Amolops were often related to geological events (e.g. the uprising of mountains and the formation of islands). By including the mitochondrial sequences from GenBank, a more comprehensive Amolops phylogeny was constructed that reflected the origin of the Chinese Amolops. Based on all these results, a dispersal scenario of the torrent frogs was hypothesized. Our research serves as the first example of using AFLP-Capture to obtain a large amount of data for shallow-scale phylogenetic and taxonomic studies, which should be useful for other nonmodel organism groups.

The uplift of the Qinghai-Tibet Plateau and glacial oscillations triggered the diversification of Tetraogallus (Galliformes, Phasianidae)

The Qinghai-Tibet Plateau (QTP) plays an important role in avian diversification. To reveal the relationship between the QTP uplift and avian diversification since the Late Cenozoic, here, we analyzed the phylogenetic relationship and biogeographical pattern of the genus Tetraogallus (Galliformes, Phasianidae) and the probable factors of speciation in the period of the QTP uplift inferred from concatenated data of four nuclear and five mitochondrial genes using the method of the Bayesian inference. Phylogenetic analysis indicated that T. himalayensis had a close relationship with T. altaicus and conflicted with the previous taxonomy of dark-bellied and white-bellied groups. The molecular clock showed that the speciation of Tetraogallus was profoundly affected by the uplift of the QTP and glacial oscillations. Biogeographic analysis suggested that the extant snowcocks originated from the QTP, and the QTP uplift and glacial oscillations triggered the diversification of Tetraogallus ancestor. Specifically, the uplift of the mountain provided a prerequisite for the colonization of snowcocks Tetraogallus as a result of the collision between the Indian and the Arab plates and the Eurasian plate, in which ecological isolation (the glacial and interglacial periods alternate) and geographical barrier had accelerated the Tetraogallus diversification process. Interestingly, we discovered hybrids between T. tibetanus and T. himalayensis for the first time and suggested that T. tibetanus and T. himalayensis hybridized after a second contact during the glacial period. Here, we proposed that the hybrid offspring was the ancestor of the T. altaicus. In conclusion, the uplift of QTP and glacial oscillations triggered the snowcocks colonization, and then, isolation and introgression hybridization promoted diversification.

Geological and Climatic Factors Affect the Population Genetic Connectivity in Mirabilis himalaica (Nyctaginaceae): Insight From Phylogeography and Dispersal Corridors in the Himalaya-Hengduan Biodiversity Hotspot

The genetic architecture within a species in the Himalaya-Hengduan Mountains (HHM) region was considered as the consolidated consequence of historical orogenesis and climatic oscillations. The visualization of dispersal corridors as the function of population genetic connectivity became crucial to elucidate the spatiotemporal dynamics of organisms. However, geodiversity and physical barriers created by paleo geo-climatic events acted vigorously to impact notable alterations in the phylogeographic pattern and dispersal corridors. Therefore, to achieve detailed phylogeography, locate dispersal corridors and estimate genetic connectivity, we integrated phylogeography with species distribution modelling and least cost path of Mirabilis himalaica (Edgew.) Heimerl in the HHM. We amplified four cpDNA regions (petL-psbE, rps16-trnK, rps16 intron, trnS-trnG), and a low copy nuclear gene (G3pdh) from 241 individuals of 29 populations. SAMOVA, genealogical relationships, and phylogenetic analysis revealed four spatially structured phylogroups for M. himalaica with the onset of diversification in late Pliocene (c. 3.64 Ma). No recent demographic growth was supported by results of neutrality tests, mismatch distribution analysis and Bayesian skyline plot. Paleo-distribution modelling revealed the range dynamics of M. himalaica to be highly sensitive to geo-climatic change with limited long-distance dispersal ability and potential evolutionary adaptation. Furthermore, river drainage systems, valleys and mountain gorges were identified as the corridors for population genetic connectivity among the populations. It is concluded that recent intense mountain uplift and subsequent climatic alterations including monsoonal changes since Pliocene or early Pleistocene formulated fragmented habitats and diverse ecology that governed the habitat connectivity, evolutionary and demographic history of M. himalaica. The integrative genetic and geospatial method would bring new implications for the evolutionary process and conservation priority of HHM endemic species.

Sky islands as foci for divergence of fig trees and their pollinators in southwest China

The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the "sky islands" of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the "sky island" complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.

The impact of Miocene orogeny for the diversification of Caucasian Epeorus (Caucasiron) mayflies (Ephemeroptera: Heptageniidae)

A common hypothesis for the high biodiversity of mountains is the diversification driven by orogeny creating conditions for rapid in situ speciation of resident lineages. The Caucasus is a young mountain system considered as a biodiversity hotspot; however, the origin and evolution of its diversity remain poorly understood. This study focuses on mayflies of the subgenus Caucasiron, one of the most diversified stenotopic mayflies inhabiting various types of streams throughout the Caucasus. Using the time-calibrated phylogeny based on two mitochondrial (COI, 16S) and three nuclear (EF-1α, wg, 28S) gene fragments, we tested the role of Caucasian orogeny in biogeography, diversification patterns, and altitudinal diversification of Caucasiron mayflies. We found that orogeny promoted the lineage diversification of Caucasiron in the Miocene. The highest diversification rate corresponding with the uplift of mountains was followed by a significant slowdown towards the present suggesting minor influence of Pleistocene climatic oscillations on the speciation. The Caucasiron lineages cluster into three principal clades originating in the Upper Miocene. We found a strong support that one of the three clades diversified via allopatric speciation in the Greater Caucasus isolated in the Parathetys Sea. The other two clades originating most likely outside the Greater Caucasus diversified towards high and low altitude, respectively, indicating possible role of climatic factors and/or passive uplift on their differentiation. Current high Caucasiron diversity in the Greater Caucasus is a result of in situ speciation and later immigration from adjacent mountain ranges after the Parathetys Sea retreat. Our phylogeny supported the monophyly of Rhithrogeninae, Epeorus s.l., Caucasiron, and Iron. Epeorus subgenus Ironopsis was found paraphyletic, with its European representatives more closely related to Epeorus s.str. than to Iron. Therefore, we re-arranged taxa treated within Ironopsis to comply with the phylogeny recovered herein.

Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

BACKGROUND AND AIMS

Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae).

METHODS

DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD).

KEY RESULTS

Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD.

CONCLUSIONS

These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes

Background

The Southern Ocean is the coldest ocean on Earth but a hot spot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation, forming >120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and the rapid expansion of the Antarctic notothenioids remain poorly understood.

Results

We sequenced and compared 2 notothenioid genomes—the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus mawsoni and the basal Patagonian robalo Eleginops maclovinus, representing the temperate ancestor. We detected >200 protein gene families that had expanded and thousands of genes that had evolved faster in the toothfish, with diverse cold-relevant functions including stress response, lipid metabolism, protein homeostasis, and freeze resistance. Besides antifreeze glycoprotein, an eggshell protein had functionally diversified to aid in cellular freezing resistance. Genomic and transcriptomic comparisons revealed proliferation of selcys–transfer RNA genes and broad transcriptional upregulation across anti-oxidative selenoproteins, signifying their prominent role in mitigating oxidative stress in the oxygen-rich Southern Ocean. We found expansion of transposable elements, temporally correlated to Antarctic notothenioid diversification. Additionally, the toothfish exhibited remarkable shifts in genetic programs towards enhanced fat cell differentiation and lipid storage, and promotion of chondrogenesis while inhibiting osteogenesis in bone development, collectively contributing to the achievement of neutral buoyancy and pelagicism.

Conclusions

Our study revealed a comprehensive landscape of evolutionary changes essential for Antarctic notothenioid cold adaptation and ecological expansion. The 2 genomes are valuable resources for further exploration of mechanisms underlying the spectacular notothenioid radiation in the coldest marine environment.

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

BACKGROUND

Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.

RESULTS

All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.

CONCLUSIONS

Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

Understanding invasion success of Pseudorasbora parva in the Qinghai-Tibetan Plateau: Insights from life-history and environmental filters

Understanding mechanisms of fish invasion success is crucial to controlling existing invasions and preventing potential future spread. Despite considerable advances in explaining successful fish invasions, little is known about how non-native fish successfully invade alpine freshwater ecosystems. Here, we explore the role of fish life history and environmental factors in contributing to invasion success of Pseudorasbora parva on the Qinghai-Tibet Plateau. We compared life history trait differences between native populations in lowland China with introduced populations in lowland Europe and the high elevation Qinghai-Tibet Plateau. Linear mixed-effects models were used to analyse life-history trait variation across elevation gradients. A random forest model was developed to identify the key environmental filters influencing P. parva invasion success. Life history characteristics differed substantially between native and introduced populations. Compared with native Chinese populations, introduced populations in lowland Europe had smaller body size, higher fecundity, smaller oocytes and earlier maturation. Introduced populations in the Qinghai-Tibet Plateau had smaller body size, lower fecundity, smaller oocytes and later maturation compared with native populations. 1-Year-Length and fecundity in all age classes of females significantly increased with increasing elevation. 2-Year-Length and 3-Year-Length of male significantly increased while maximal longevity and length at first maturity were significantly decreased with the elevation gradient. Habitat type, annual mean temperature, elevation, annual precipitation and precipitation seasonality, were the 5 most important predictors for the occurrence of the P. parva. Our study indicates that invasive P. parva adopt different life history strategies on the plateau compared with invasive populations at low elevations, highlighting that more studies are required for a better understanding of biological invasion under extreme conditions. Considering the ongoing hydrologic alteration and climate change, our study also highlighted that P. parva may expand their distribution range in the future on the Qinghai-Tibet Plateau.

Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China

Southwestern (SW) China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that influences the genetic structure of the resident populations of plants and animals. Iron walnut (Juglans regia subsp. sigillata) is a deciduous tree species endemic to this region of China and cultivated there for its edible nuts. We sampled 36 iron walnut populations from locations throughout the species' range in SW China and genotyped a total of 765 individuals at five chloroplast DNA regions and 22 nuclear microsatellite loci. Species distribution models were produced to predict the evolution and historical biogeography of iron walnut and to estimate the impacts of climate oscillations and orographic environments on the species' demography. Our results indicated that J. regia subsp. sigillata had relatively low genetic diversity, high interpopulation genetic differentiation, and asymmetric interpopulation gene flow. Based on DIYABC analysis, we identified two lineages of J. sigillata in southwestern China. The lineages (subpopulations) diverge during the last glacial period (~1.34 Ma). Southwestern China was a glacial refuge during the last glacial period, but increasingly colder and arid climates might have fostered the fragmentation of J. regia subsp. sigillata within this refugium. Finally, we found that recent habitat fragmentation has led to a reduction in population connectivity and increased genetic differentiation by genetic drift in isolated populations. Our results support a conclusion that geological and climatic factors since the Miocene triggered the differentiation, evolutionary origin, and range shifts of J. sigillata in the studied region.

Concealed truth: Modeling reveals unique Quaternary distribution dynamics and refugia of four related endemic keystone Abies taxa on the Tibetan Plateau

Understanding the factors driving the Quaternary distribution of Abies in the Tibetan Plateau (TP) is crucial for biodiversity conservation and for predicting future anthropogenic impacts on ecosystems. Here, we collected Quaternary paleo-, palynological, and phylogeographical records from across the TP and applied ecological niche models (ENMs) to obtain a profound understanding of the different adaptation strategies and distributional changes in Abies trees in this unique area. We identified environmental variables affecting the different historical biogeographies of four related endemic Abies taxa and rebuilt their distribution patterns over different time periods, starting from the late Pleistocene. In addition, modeling and phylogeographic results were used to predict suitable refugia for Abies forrestii, A. forrestii var. georgei, A. fargesii var. faxoniana, and A. recurvata. We supplemented the ENMs by investigating pollen records and diversity patterns of cpDNA for them. The overall reconstructed distributions of these Abies taxa were dramatically different when the late Pleistocene was compared with the present. All Abies taxa gradually receded from the south toward the north in the last glacial maximum (LGM). The outcomes showed two well-differentiated distributions: A. fargesii var. faxoniana and A. recurvata occurred throughout the Longmen refuge, a temporary refuge for the LGM, while the other two Abies taxa were distributed throughout the Heqing refuge. Both the seasonality of precipitation and the mean temperature of the driest quarter played decisive roles in driving the distribution of A. fargesii var. faxoniana and A. recurvata, respectively; the annual temperature range was also a key variable that explained the distribution patterns of the other two Abies taxa. Different adaptation strategies of trees may thus explain the differing patterns of distribution over time at the TP revealed here for endemic Abies taxa.

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.

Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot

The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. Here, we investigate factors driving intraspecific divergence within a HDM alpine species Salix brachista (Cushion willow), a common component of subnival assemblages. We produce a high-quality genome assembly for this species and characterize its genetic diversity, population structure and pattern of evolution by resequencing individuals collected across its distribution. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene. These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Since intraspecific divergence is often the first step toward speciation, the same factors can be important contributors to the high alpine species diversity in the HDM.

Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages

BACKGROUND

Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures.

RESULTS

Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America.

CONCLUSIONS

Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.

Phylogenomic analysis reveals multiple evolutionary origins of selfing from outcrossing in a lineage of heterostylous plants

Evolutionary transitions from outcrossing to selfing often occur in heterostylous plants. Selfing homostyles originate within distylous populations and frequently evolve to become reproductively isolated species. We investigated this process in 10 species of Primula section Obconicolisteri using phylogenomic approaches and inferred how often homostyly originated from distyly and its consequences for population genetic diversity and floral trait evolution. We estimated phylogenetic relationships and reconstructed character evolution using the whole plastome comprised of 76 protein-coding genes. To investigate mating patterns and genetic diversity we screened 15 microsatellite loci in 40 populations. We compared floral traits among distylous and homostylous populations to determine how phenotypically differentiated homostyles were from their distylous ancestors. Section Obconicolisteri was monophyletic and we estimated multiple independent transitions from distyly to homostyly. High selfing rates characterised homostylous populations and this was associated with reduced genetic diversity. Flower size and pollen production were reduced in homostylous populations, but pollen size was significantly larger in some homostyles than in distylous morphs. Repeated transitions to selfing in section Obconicolisteri are likely to have been fostered by the complex montane environments that species occupy. Unsatisfactory pollinator service is likely to have promoted reproductive assurance in homostyles leading to subsequent population divergence through isolation.

Phylogeny, origin and dispersal of Saussurea (Asteraceae) based on chloroplast genome data

Saussurea is one of the largest genera of the tribe Cardueae of Asteraceae, comprising about 460 species from the Northern Hemisphere with most species distributed in QTPss and adjacent areas. Here, we established a well-supported phylogenetic framework for Saussurea based on whole chloroplast genomes of 136 taxa plus 16 additional taxa of Cardueae using Bayesian inference and Maximum Likelihood. Our phylogenetic results are inconsistent with previous subgeneric classifications of Saussurea. We nearly completely delimited subgen. Eriocoryne, and found that subgen. Theodorea, subgen. Saussurea section Laguranthera and Rosulascentes are closely related to each other. Based on our phylogenetic results, we performed biogeographic analyses and inferred that the genus Saussurea arose during early-middle Miocene within the Hengduan Mountains. We expect that landscape heterogeneity within the QTPss and adjacent areas, such as the Hengduan Mountains, played an important role in the evolution of Saussurea. Following its evolutionary origin, the genus underwent rapid diversification in situs and dispersed northwards in several migrational patterns. Both continuous uplift of the QTPss and adjacent areas as well as global cooling since mid-Miocene probably led to geographic expansion and diffusion of Saussurea, with the latter, in particular, resulting in the northward dispersal.

Building mountain biodiversity: Geological and evolutionary processes

Mountain regions are unusually biodiverse, with rich aggregations of small-ranged species that form centers of endemism. Mountains play an array of roles for Earth’s biodiversity and affect neighboring lowlands through biotic interchange, changes in regional climate, and nutrient runoff. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with distinct opportunities for coexistence and persistence of lineages, shaped by long-term climatic changes interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology—notably, areas comprising mafic and ultramafic lithologies, rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving.

Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae)

BACKGROUND

Triplophysa stoliczkae is the most widespread species in the genus Triplophysa and may have originated from morphological convergence. To understand the evolutionary history of T. stoliczkae, we employed a multilocus approach to investigate the phylogenetics and the morphological evolution of T. stoliczkae on the Qinghai-Tibetan Plateau.

RESULTS

All phylogenetic analyses (two mitochondrial and five nuclear loci), a genealogical sorting index and species tree inferences suggested that T. stoliczkae consists of distinct lineages that were not closest relatives. The time estimation indicated that the divergence events between "T. stoliczkae" and other Triplophysa species occurred from approximately 0.10 to 4.51 Ma. The ancestral state analyses supported the independent evolution of T. stoliczkae morphology in distinct lineages. The morphometric analysis and convergence estimates demonstrated significant phenotypic convergence among "T. stoliczkae" lineages.

CONCLUSIONS

Triplophysa stoliczkae includes 4 different lineages with similar morphologies. The increasingly harsh environments that have occurred since the Pliocene have driven the occurrences of scrape-feeding fish in the genus Triplophysa. Morphological adaptations associated with scrape-feeding behavior resulted in convergences and the artificial lumping of four different species in the nominal taxon T. stoliczkae. A taxonomic revision for T. stoliczkae is needed.

Altitudinal biodiversity patterns of seed plants along Gongga Mountain in the southeastern Qinghai-Tibetan Plateau

The mechanisms underlying elevation patterns in species and phylogenetic diversity remain a central issue in ecology and are vital for effective biodiversity conservation in the mountains. Gongga Mountain, located in the southeastern Qinghai-Tibetan Plateau, represents one of the longest elevational gradients (ca. 6,500 m, from ca. 1,000 to 7,556 m) in the world for studying species diversity patterns. However, the elevational gradient and conservation of plant species diversity and phylogenetic diversity in this mountain remain poorly studied. Here, we compiled the elevational distributions of 2,667 native seed plant species occurring in Gongga Mountain, and estimated the species diversity, phylogenetic diversity, species density, and phylogenetic relatedness across ten elevation belts and five vegetation zones. The results indicated that species diversity and phylogenetic diversity of all seed plants showed a hump-shaped pattern, peaking at 1,800-2,200 m. Species diversity was significantly correlated with phylogenetic diversity and species density. The floras in temperate coniferous broad-leaved mixed forests, subalpine coniferous forests, and alpine shrublands and meadows were significantly phylogenetically clustered, whereas the floras in evergreen broad-leaved forests had phylogenetically random structure. Both climate and human pressure had strong correlation with species diversity, phylogenetic diversity, and phylogenetic structure of seed plants. Our results suggest that the evergreen broad-leaved forests and coniferous broad-leaved mixed forests at low to mid elevations deserve more conservation efforts. This study improves our understanding on the elevational gradients of species and phylogenetic diversity and their determinants and provides support for improvement of seed plant conservation in Gongga Mountain.

Complex population evolutionary history of four cold-tolerant Notopterygium herb species in the Qinghai-Tibetan Plateau and adjacent areas

Historical geological and climatic events are the most important drivers of population expansions/contractions, range shifts, and interspecific divergence in plants. However, the species divergence and spatiotemporal population dynamics of alpine cold-tolerant herbal plants in the high-altitude Qinghai-Tibetan Plateau (QTP) and adjacent areas remain poorly understood. In this study, we investigated population evolutionary history of four endangered Notopterygium herb species in the QTP and adjacent regions. We sequenced 10 nuclear loci, 2 mitochondrial DNA regions, and 4 chloroplast DNA regions in a total of 72 natural populations from the 4 species, and tested the hypothesis that the population history of these alpine herbs was markedly affected by the Miocene-Pliocene QTP uplifts and Quaternary climatic oscillations. We found that the four Notopterygium species had generally low levels of nucleotide variability within populations. Molecular dating and isolation-with-migration analyses suggested that Notopterygium species diverged ~1.74-7.82 million years ago and their differentiation was significantly associated with recent uplifts of the eastern margin of the QTP. In addition, ecological niche modeling and population history analysis showed that N. incisum and N. franchetii underwent considerable demographic expansions during the last glacial period of the Pleistocene, whereas a demographic contraction and a expansion occurred for N. forrestii and N. oviforme during the antepenultimate interglacial period and penultimate glacial period, respectively. These findings highlight the importance of geological and climatic changes during the Miocene-Pliocene and Pleistocene as causes of species divergence and changes in population structure within cold-tolerant herbs in the QTP biodiversity hotspot.