The effect of Hengduan Mountains Region (HMR) uplift to environmental changes in the HMR and its eastern adjacent area: Tracing the evolutionary history of Allium section Sikkimensia (Amaryllidaceae)

Divergence of alpine plant populations of three Gentianaceae species in the Qinling sky Island

BACKGROUND

Known for their unique biodiversity, the Qinling Mountains are considered the only area in which alpine biomes occur in central China. Given that the alpine biomes are particularly sensitive to global warming, understanding how alpine plants respond to climatic fluctuations is essential for the evolution and conservation of biodiversity. To address this issue, three alpine species of the Gentianaceae (Gentiana crassuloides, G. hexaphylla and Swertia bifolia) that represent different life types and diverse genera were selected.

RESULTS

Genetic clustering analysis according to around 33,317 to 185,133 SNPs showed that the Qinling population was a separate lineage within each species. A high level of genetic differentiation was observed among the Qinling populations and the other populations of each species. Divergence time estimation based on plastomes and approximate Bayesian computation based on genomic SNPs showed that Qinling populations of the three Gentianaceae species originated at different periods under various patterns including primary source and hybridization. Significant signals of isolation by distance and isolation by environment were found in all three species. The redundancy and gradient forest analyses revealed that several temperature- and precipitation-related variables mainly contributed to shaping the genetic differentiation among the Qinling populations and others, indicating that the three species exhibited a similar pattern of adaptations to local environments.

CONCLUSIONS

This study unveiled the unique genetic and evolutionary features of the Qinling populations of these three species and elucidated the contributing role of both the environmental gradient and geographical isolation in genetic differentiation, which scientifically supports future conservation efforts.

Morphology, phylogeography, phylogeny, and taxonomy of Cyclorhiza (Apiaceae)

Background

The genus Cyclorhiza is endemic to China and belongs to the Apiaceae family, which is widely distributed in the Himalaya-Hengduan Mountains (HHM) region. However, its morphology, phylogeny, phylogeography, taxonomy, and evolutionary history were not investigated due to insufficient sampling and lack of population sampling and plastome data. Additionally, we found that Seseli purpureovaginatum was not similar to Seseli members but resembled Cyclorhiza species in morphology, indicating that the taxonomic position of S. purpureovaginatum needs to be re-evaluated.

Methods

First, we observed the morphology of the genus. Second, we newly sequenced four plastomes and conducted comparative analyses. Third, we used the newly sequenced internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) (matK, trnQ-rps16, and trnD-trnT) from 27 populations totaling 244 individuals to explore the genetic diversity and structure. Finally, we performed the phylogenetic analyses based on three datasets (plastome data, ITS sequences, and haplotypes) and estimated the origin and divergence time of the genus.

Results and discussion

The morphology of Cyclorhiza plants and S. purpureovaginatum was highly similar, and their plastomes in structure and features were conserved. The genus possessed high genetic diversity and significant lineage geographic structure, which may be associated with the long-term evolutionary history, complex terrain and habitat, and its sexual reproduction mode. The genus Cyclorhiza originated in the late Eocene (36.03 Ma), which was closely related to the early uplift of the Qinghai-Tibetan Plateau (QTP) and Hengduan Mountains (HDM). The diversification of the genus occurred in the late Oligocene (25.43 Ma), which was largely influenced by the colonization of the newly available climate and terrain. The phylogenetic results showed that Cyclorhiza species clustered into a separate clade and S. purpureovaginatum nested within Cyclorhiza. Cyclorhiza waltonii was sister to Cyclorhiza peucedanifolia, and Cyclorhiza puana clustered with S. purpureovaginatum. Thus, based on the morphology, plastome analyses, and phylogenetic evidence, S. purpureovaginatum should be transferred to Cyclorhiza. All these evidences further supported the monophyly of the genus after including S. purpureovaginatum. Finally, we clarified the generic limits of Cyclorhiza and provided a species classification key index for the genus. In conclusion, the study comprehensively investigated the morphology, phylogeography, phylogeny, taxonomy, and evolution of the genus Cyclorhiza for the first time.

Genome assembly of an endemic butterfly (Minois Aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat

BACKGROUND

The Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the arid valley remain poorly understood. Minois aurata, an endemic butterfly species found exclusively in the arid valley of the upper Minjiang River, represents an attractive model system for studying adaptive evolutionary mechanisms to arid valley environments.

RESULTS

Here, we present the first chromosome-level genome assembly for Minois aurata, with a total size of approximately 609.17 Mb, and a scaffold N50 size of 23.88 Mb. These scaffolds were further clustered and anchored onto 29 chromosomes based on Hi-C data. A total of 16,163 protein-coding genes were predicted, of which 91.83% were functionally annotated. The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata, potentially aiding its adaptation to environmental conditions. Phylogenomic analyses based on 3,785 single-copy genes revealed that M. aurata is most closely related to Hipparchia semele. Further mitochondrial genome analysis of four Minois species placed M. aurata in a basal position within the genus, supporting it as an independent species. A total of 185 rapidly evolving and 232 specific gene families were identified in M. aurata. Functional enrichment analysis indicated that these gene families were mainly associated with ultraviolet radiation, heat and hypoxia responses. We also identified 234 positive selected genes in M. aurata, some of which are related to compound eye photoreceptor development, osmotic stress, and light stimulus response. Demographic analysis indicated that the effective population size of M. aurata decreased around 0.4 and 0.04 million years ago, respectively, coinciding with the localized sub-glaciation.

CONCLUSION

The chromosome-level genome offers a comprehensive genomic basis for understanding the evolutionary and adaptive strategies of Minois aurata in the unique arid valley environment of the Hengduan Mountains, while also providing valuable insights into the broader mechanisms of organism adaptation to such habitats.

Speciation and diversification of the Bupleurum (Apiaceae) in East Asia

Bupleurum, belonging to the Apiaceae, is widely distributed across the Eurasian continent. The origin and species diversification of Bupleurum in East Asia, remain incompletely resolved due to the limited samples in previous studies. To address these issues, we have reconstructed a robust phylogenetic framework for Bupleurum in East Asia based on the ITS and three plastid genes. Our phylogenetic analysis confirms the monophyly of Bupleurum with strong support. Both ITS and chloroplast dataset divided the Bupleurum in East Asia into East Asia Group I and East Asia Group II in this study. The divergence time and ancestral area reconstruction of ITS dataset indicated that the Bupleurum originated in the Mediterranean basin and its adjacent areas around 50.33 Ma. subg. Penninervia and subg. Bupleurum diverged at about 44.35 Ma, which may be related to the collision of India with the Eurasian continent. Both East Asia Group I and East Asia Group II originated from a common ancestor in the Mediterranean, East Asia Group I divergence around 12.95 Ma; East Asia Group II divergence around 13.32 Ma. The character reconstruction showed that the morphological characters and altitude distribution analyzed in this study exhibit a scattered distribution in East Asian Group I and East Asian Group II. Additionally, diversification rate analysis shows that the East Asian Group I and East Asian Group II exhibited no significant shifts in diversification rates in the evolutionary history according to ITS and combined dataset. Both molecular and morphological data supports that East Asian Bupleurum is a museum taxon, meaning that the species diversity of East Asian Bupleurum has gradually accumulated over time.

Biological features and quality comprehensive analysis of twelve germplasm resources of the genus Allium from Tibet

Introduction

Allium is important vegetables and seasonings in China, Tibet is rich in unique resources of the genus Allium, but lacks development and utilization.

Methods

We compared the biological features and comprehensively evaluating the quality of twelve germplasm resources of the genus Allium collected from Tibet.

Results

The results revealed that nine germplasm resources were bolting and bloom normally except for SC015, SC019, and SC048, all twelve germplasm resources were able to vegetative growth. The individual differences in moisture, soluble sugar, and protein content among the twelve germplasm resources were relatively small, with pyruvic acid content ranging from 0.11 to 1.12 mg/g and a large variation coefficient. A total of 8 categories and 97 volatile compounds were detected in twelve germplasm resources, the majority possessed the highest proportions of aldehydes and organosulfur compounds, but there were certain differences between the different Allium species. Additionally, 11 to 16 types of free amino acids were present in all germplasm resources, proline exhibited the highest content. The total content of essential and non-essential amino acids in SC009 was the highest. Carbon (C) accounted for the largest proportion of all elements, and the contents of other mineral elements varied greatly among the different plants.

Conclusion

In conclusion, combined with biological performance and comprehensive evaluation of quality, SC009 is the excellent germplasm resource suitable for growth and capable of reproduction with good quality. These results improved the exploitation and utilization of the genus Allium in Tibet, as well as provided germplasm resources for high-quality breeding of the genus Allium.

Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data

Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples of F. cirrhosa and its relatives collected from various regions, encompassing the majority of wild populations across diverse geographical areas. The results indicate abundant variations in 46 accessions including 1659 single-nucleotide polymorphisms and 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, and rpl32-trnL) were identified. Phylogenetic and network analysis, population structure analysis, and principal component analysis showed that the 46 accessions formed five clades with significant divergence, which were related to their geographical distribution. The regions spanning from the southern Hengduan Mountains to the Qinghai-Tibet Plateau exhibited the highest levels of genetic diversity. F. cirrhosa and its relatives may have suffered a genetic bottleneck and have a relatively low genetic diversity level. Moreover, geographical barriers and discrete patches may have accelerated population divergence. The study offers novel perspectives on the phylogeny, genetic diversity, and population structure of F. cirrhosa and its relatives, information that can inform conservation and utilization strategies in the future.

Incomplete lineage sorting and gene flow within Allium (Amayllidaceae)

The phylogeny and systematics of the genus Allium have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make Allium a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 Allium species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus Allium. We presented clear evidence for substantial ILS across the phylogeny of Allium. Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. Butomissa as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of Allium. This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled Allium species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.

Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae)

Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid-polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.

Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution

In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking. In this study, we sequenced 18 Allioideae plastomes and combined them with publicly available data (a total of 41 plastomes), including 21 Allioideae species, 1 Agapanthoideae species, 14 Amaryllidoideae species, and 5 Asparagaceae species. Comparative analyses were performed including basic characteristics of genome structure, codon usage, repeat elements, IR boundary, and genome divergence. Phylogenetic relationships were detected using single-copy genes (SCGs) and ribosomal internal transcribed spacer sequences (ITS), and the branch-site model was also employed to conduct the positive selection analysis. The results indicated that all Amaryllidaceae species showed a highly conserved typical tetrad structure. The GC content and five codon usage indexes in Allioideae species were lower than those in the other two subfamilies. Comparison analysis of Bayesian and ML phylogeny based on SCGs strongly supports the monophyly of three subfamilies and the sisterhood among them. Besides, positively selected genes (PSGs) were detected in each of the three subfamilies. Almost all genes with significant posterior probabilities for codon sites were associated with self-replication and photosynthesis. Our study investigated the three subfamilies of Amaryllidaceae at the whole chloroplast genome level and suggested the key role of selective pressure in the adaptation and evolution of Amaryllidaceae.

Distribution patterns of Chinese Cixiidae (Hemiptera, Fulgoroidea), highlight their high endemic diversity

Background

Cixiidae are small strictly phytophagous hemipteran insects worldwide distributed. Ecology and systematics of Chinese fauna remains poorly investigated. For instance, does their distribution follows the patterns of biogeogaphical distribution established for their host plants or other related-taxa because they are all obligatory phytophagous taxa? Do they follow the usual distributional Chinese realms and boundaries already recognized? Which zoogeographical Chinese regions and connections between them do they depict. To investigate these issues, we provide here a referenced and comprehensive checklist of the 250 cixiid species currently reported from China (77 new records), with their precise distribution at the regional level. In the 8 Chinese main zoogeographical regions usually recognized and 2 adjacent areas, we analyzed further their diversity at the tribal, generic, and specific levels using a non-metric multidimensional scaling and an unweighted pairwise group analysis using an arithmetic mean cluster analyses. The observed distribution patterns shown that an intercalary Sino-Japanese realm is recognisable between the Palaearctic and Oriental realms. At the regional level, the South China region clusters more closely with the Southwest, Central and North China regions. Taiwan, clearly separated from the South China region and mainland China, is more closely related to the Qinghai-Tibet region and Indochina countries. Although Central and South China regions remain close to each other, the Qinghai-Tibet region appears singularly different.

New information

An updated checklist of the 250 Cixiidae species, known to occur in China and counting for 10% of the Chinese planthopper fauna, is presented based on literature, recent collections, and museum records. More than 400 records distributed among the 28 provinces and 8 regions in China are extensively provided, including 77 new records. Of these, more than 80% of the species (205 species, 82%) have been only reported from China, and most of them are endemic species, which could reflects the great diversity degree of the Chinese regions and local biotypes highlights the uniqueness of this fauna. These species are found in 8 Chinese zoogeographical regions: The Taiwan region is the most diversified with 161 species and the highest rate of endemic species (69.57%), followed by South China (78 species, 17.95%), Central China (60 species, 33.33%), Southwest China (43 species, 39.53%), North China (29 species, 34.48%), Qinghai-Tibet region (10 species, 20%), Northeast China (8 species, 12.5%), and 5 species found in the Inner Mongolia-Xinjiang region that are not endemic ones. Endemism was analyzed for each region and repeated for species distribution patterns across them, 9 being bi-regionally and tri-regionally distributed. The South China-Taiwan pattern is the most richest one, followed by the Central-South China-Taiwan pattern. Semonini and Pentastirini tribes are widespread among all the zoological regions, representing respectively 21.20% and 17.20% of all the species, while Cixiini being is the most common tribe with 45.20%, remains absent from the North-Eastern China region. Andini with only 5.20% of the species is distributed in the Sino-Japanese - Oriental Region; Eucarpini (6.40%) and Borysthenini (2.00%) are mainly concentrated in the south of the Qingling Mountain-Huai River. The remaining four tribes, Bennini (0.40%), Briixini (0.80%), Oecleini (1.20%) and Stenophlepsiini (0.40%) are relatively rare and restricted to Taiwan. At the generic level, Kuvera (7.2%) is the most widely distributed genus in China while Cixius, Betacixius, Kuvera, Oecleopsis and Andes are the more diversified. One genus (Oliparisca) is distributed only in the Tibet region, while 10 genera are distributed only in the Taiwan region. In addition, nearly half of the genera (16 genera, 48.48%) are distributed south of the Palearctic/Oriental boundary. A non-metric multidimensional scaling and an unweighted pairwise group method analysis using arithmetic mean clustering based on the Jaccard similarity coefficient matrix support a Palaearctic/Sino-Japanese boundary and a South China region closer to the Southwest, Central and North China regions. The Taiwan region appears clearly separated from the South China region and to mainland China, and more closely related to the Qinghai-Tibet region and Indochina countries. The Central and South China regions appear close to each other, but the Qinghai-Tibet region is singularly isolated.

Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

Modern accumulations of genetic data offer unprecedented opportunities for understanding the systematic classification and origins of specific groups of organisms. The genus Sinocyclocheilus is among the most cave abundant genera in Cyprinidae, with 76 recognized species, belonging to four species groups. Recent phylogenetic studies have shown that the classification of species groups within the genus Sinocyclocheilus remains controversial. In this study, we constructed a sequence supermatrix of 26 species from four species groups of the genus Sinocyclocheilus using the mitochondrial genome to reveal phylogenetic relationships, historical biogeography and patterns of species diversification in the genus Sinocyclocheilus. Phylogenetic analysis strongly supports the monophyletic groups of the three species groups (S. jii, S. cyphotergous, and S. tingi groups) except the S. angularis group. Phylogenetic analysis showed that S. anshuiensis and S. microphthalmus, which were recognized as numbers of S. angularis group, formed a strongly supported independent clade. Therefore, we propose a new species group, the S. microphthalmus group, which contains S. anshuiensis and S. microphthalmus. Biogeographic reconstruction suggests that the living Sinocyclocheilus may have originated in north-central Guangxi at the late Eocene and dispersed outward after a vicariance at 32.31 Million years ago (Ma). Early diversification is focused on the late Oligocene (ca. 25 Ma), which is related to the second uplift of the Qinghai-Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary. Our results suggest that two uplifts of the Qinghai-Tibetan Plateau and climate change in the Miocene may have influenced the diversification of the Sinocyclocheilus lineage. This article is protected by copyright. All rights reserved.

Out of the Qinghai-Tibetan Plateau and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidated the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the Qinghai-Tibetan Plateau (QTP) and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4-3 million years ago (Mya). Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence of Chamaesium (Apiaceae)

Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.

Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers

Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium.

Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences

BACKGROUND AND AIMS

The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study.

METHODS

In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families.

RESULTS

Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species.

CONCLUSIONS

Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.

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.

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.

Polyploidy promotes species diversification of Allium through ecological shifts

Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.