Miao Sun

Huazhong Agricultural University | HZAU · College of Horticulture and Forestry

A revision of Elaeagnus L. for mainland China is provided based on field observations and herbarium studies. Forty-two morphological characters are selected and coded, then the matrix is prepared following cluster analysis. Morphological characters and species delimitation are re-evaluated resulting in the recognition of 36 species, one subspecies...

Rosidae, a clade of ∼ 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas o...

High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins3,4, and...

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical glo...

Across the globe, tree species are under high anthropogenic pressure. Risks of extinction are notably more severe for species with restricted ranges and distinct evolutionary histories. Here, we use a global dataset covering 41,835 species (65.1% of known tree species) to assess the spatial pattern of tree species’ phylogenetic endemism, its macroe...

The monotypic genus Pseudomarrubium is perhaps the most poorly understood taxon within the subfamily Lamioideae (Lamiaceae). While advances in molecular phylogenetics have clarified the phylogeny and taxonomy of Lamioideae, the systematic placement of Pseudomarrubium remains unclear, as it has never been tested using molecular phylogenetic analyses...

Regions harbouring high unique phylogenetic diversity (PD) are priority targets for conservation. Here, we analyse the global distribution of plant PD, which remains poorly understood despite plants being the foundation of most terrestrial habitats and key to human livelihoods. Capitalising on a recently completed, comprehensive global checklist of...

COLE TCH, GARDNER EM, SUN M 孙苗 (2023) MORACEAE 桑科系统发育海报 © COLE, GARDNER, SUN 2023 (CC-BY), Chinese version of: Cole, Gardner (2023) MORACEAE Phylogeny Poster (MorPP) • 亚科，族以及属具祖征/衍征和(非)诊断特征 • 基于分子系统进化树 • 48属，约1125种 • 系统发育、分类以及特征性状摘自下面参考文献 • 枝长无意义，不代表具体分化时间 • 分支上列出的性状，并不是该分支的所有成员都有

As Earth's climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimila...

Due to intensified human pressure and climate change, ex situ conservation measures have become essential for conserving Earth's remaining biodiversity, but the development of targeted ex situ conservation strategies based on conservation gaps analysis is often a major challenge. Here, we used a dated phylogeny including 95.70 % of the Chinese vasc...

Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody...

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia–eastern North America (EA−ENA disjuncts) and their associ...

The Darwinian shortfall, i.e. the lack of knowledge of phylogenetic relationships, significantly impedes our understanding of evolutionary drivers of global patterns of biodiversity. Spatial bias in the Darwinian shortfall, where phylogenetic knowledge in some regions is more complete than others, could undermine eco‐ and biogeographic inferences....

China has many threatened plant species, which are exposed to environmental degradation and other anthropogenic pressures. We assessed support for potential extinction pathways in Chinese angiosperm genera and quantified possible threats to phylogenetic diversity. We compiled a database and phylogeny for 27,409 Chinese angiosperm species in 2,453 g...

[This corrects the article DOI: 10.1371/journal.pone.0252581.].

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In th...

Earlier phylogenetic studies in the genus Pinguicua (Lentibulariaceae) suggested that the species within a geographical region was rather monophyletic, although the sampling was limited or was restricted to specific regions. Those results conflicted with the floral morphology-based classification, which has been widely accepted to date. In the curr...

Building and dating nearly comprehensive phylogenetic trees for large clades remains a monumental task. Lamiaceae are the sixth largest flowering plant family with over 7,000 species, and despite wide interest in the family, a comprehensive phylogenetic framework is still lacking. The Open Tree of Life has made great strides connecting subtrees bas...

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In th...

In response to our paper on the evolutionary history of the Chinese flora, Qian suggests that certain features of the divergence time estimation employed might have led to biased conclusions in Lu et al (2018). Here, we consider Qian's specific criticisms, explore the extent of uncertainty in the data and demonstrate that (i) no systematic bias tow...

Premise: Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements t...

Catnip or catmint ( Nepeta spp.) is a flowering plant in the mint family (Lamiaceae) famed for its ability to attract cats. This phenomenon is caused by the compound nepetalactone, a volatile iridoid that also repels insects. Iridoids are present in many Lamiaceae species but were lost in the ancestor of the Nepetoideae, the subfamily containing Ne...

A major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these patterns are formed. Few studies have focused on the ancient, species-rich Magnoliales clade and its diversification pattern. Within Magnoliales, the pantropically distributed Annonaceae are by far the most genus-rich and...

Premise of the Study: Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification rates. These now-common approaches typically (1) are characterized by incomplete coverage without explicit sampling methodologies, and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic p...

Current advances in sequencing technology have greatly increased the availability of sequence data from public genetic databases. With data from GenBank, we assemble and phylogenetically investigate a 19,740-taxon, five-locus supermatrix (i.e., atpB, rbcL, matK, matR, and ITS) for rosids, a large clade containing over 90,000 species, or approximate...

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, experti...

Background A major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these patterns are formed. Few studies have focused on the ancient, species-rich Magnoliales clade and its diversification pattern. Within Magnoliales, the pantropically distributed Annonaceae are by far the most genu...

Recent studies have detected strong phylogenetic signals in tree–fungus associations for diseased leaves and mycorrhizal symbioses. However, the extent of plant phylogenetic constraints on the free-living soil mycobiome remains unknown, especially at broad geographic scales. Here, 343 soil samples were collected adjacent to individual tree trunks,...

Should we build our own phylogenetic trees based on gene sequence data or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort and exper...

Recently Ulloa Ulloa et al. (2017) published a 2600-page online checklist of the New World vascular plants (the Checklist hereafter) that includes 124,993 species, 6227 genera, and 355 families associated with incomplete elementary taxonomy as well as with the distributional data provided for every species (Ulloa Ulloa et al., 2017). Givnish (2017)...

Recently Ulloa Ulloa et al. (2017) published a 2600-page online checklist of the New World vascular plants (the Checklist hereafter) that includes 124,993 species, 6227 genera, and 355 families associated with incomplete elementary taxonomy as well as with the distributional data provided for every species (Ulloa Ulloa et al., 2017). Givnish (2017)...

Information of RAD-seq data.

DeltaK generated by Structure Harvester in population clustering analysis.

Juglans species have considerable ecological and economic value worldwide. In China, Wenwan walnuts have been collected by aristocrats and noblemen for more than 2000 years. As a diversity center of Asian Juglans, five species are widely distributed in China. The most famous of these is Mahetao (J. hopeiensis), which is an uncharacterized species t...

Using phylogenetic approaches to test hypotheses on a large scale, in terms of both species sampling and associated species traits and occurrence data—and doing this with rigor despite all the attendant challenges—is critical for addressing many broad questions in evolution and ecology. However, application of such approaches to empirical systems i...

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 fa...

Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compar...

Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. • Methods and Results: Using software packages and custom scripts, we id...

There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen-fixing clade: (i) a genu...

By far, the interordinal relationships in rosids remain poorly resolved. Previous studies based on chloroplast, mitochondrial, and nuclear DNA has produced conflicting phylogenetic resolutions that has become a widely concerned problem in recent phylogenetic studies. Here, a total of 96 single-copy nuclear gene loci were identified from the KOG (eu...

The term “Tree of Life” was first used by Charles Darwin in 1859 as a metaphor for describing phylogenetic relationships among organisms. Over the past three decades, the recognized tree of life has improved considerably in overall size and reliability due to an increase in diversity of character resources, a dramatic growth in useable data, and th...

Summary Eight names in five genera Delphinium (Ranunculaceae), Lindernia and Mimulicalyx (Scrophulariaceae), Sorbus and Spiraea (Rosaceae) from China were not validly published because two gatherings were simultaneously designated as types in the protologues, or were simultaneously cited, without indicating the type in the protologues. These eight...