Yongshuai Sun

Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences · Plant evolutionary ecology research group

Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in the conifer Picea brachytyla. Our analyses revealed non-sister relationships for two lineages of P. brachytyla, with the southern lineage being placed wi...

Background and aims: Hybridisation increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridisation history were examined within one Chinese hazel species complex (Corylus chinensis-Corylus fargesii). Two species including four varieties have already been described for this c...

Rhamnella intermedia, a new evergreen species from southwest Guangxi, is described and illustrated in this study. This species is similar to R. brachycarpa by the size and ratio of length to width of dried fruit and seeds, by which it differs from R. rubrinervis and R. tonkinensis. However, it differs from R. brachycarpa by rarely mucronate seed ap...

Hybridization can drive speciation. We examine the hypothesis that Castanea henryi var. omeiensis is an evolutionary lineage that originated from hybridization between two near-sympatric diploid taxa, C. henryi var. henryi and C. mollissima. We produce a high-quality genome assembly for mollissima and characterize evolutionary relationships among r...

Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using popu...

Rhamnella brachycarpa Z. Qiang Lu & Y. Shuai Sun, a new evergreen woody species from Hainan Island, is described and illustrated. The specimens of this new species have previously been identified and placed under R. rubrinervis (H. Lév.) Rehder, with which it shares evergreen leaves, erect and climbing habits and axillary flowering branches with br...

The well‐known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry may postdate the species divergence. We examined this hypothesis using DNA sequence data from 3 chloroplast fragments...

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Applying whole-transcriptome sequencing and population genetic analyses, we present an example of ancient in...

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally. While sources of resistance may be available in related species, or among surviving trees, introgression o...

The complete chloroplast genome sequence of Parashorea chinensis, an endangered large tree species in the northern edge of tropical Asia, is determined in this study. The total genome size is 152,002 bp, containing a large single copy (LSC) region (84,094 bp) and a small single copy region (20,003), which were separated by two inverted repeat (IRs)...

Background With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the...

Nonbifurcating divergence caused by introgressive hybridization is continuously reported for groups of closely related species. In this study, we aimed to reconstruct the genome‐scale classification of deep lineages of the conifer genus Picea, establish their phylogenetic relationships and test the bifurcating hypothesis between deeply branching li...

An increasing number of species are thought to have originated by homoploid hybrid speciation (HHS), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea, a conifer in the Qinghai‐Tibet Plateau (QTP), originated through HHS from P. likiangensis and P. wilsonii. To investigate this origin in...

The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Evidence of genetic exchange between diverging taxa is reported frequently, although most studies fail to show how hybridization and introgression contribute to the adaptation and differentiation of introgressed taxa. Here, we...

Although China and India are the two largest tea-producing countries, the domestication origin and breeding history of the tea plant in these two countries remain unclear. Our previous study suggested that the tea plant includes three distinct lineages (China type tea, Chinese Assam type tea and Indian Assam type tea), which were independently dome...

SSR dataset for Camellia taliensis.

Details of the haplotypes obtained with cpDNA sequencing.

Collection Information of the 402 tea samples used in the current study.

Best K values for STRUCTURE analysis using two methods of (A) ΔK and (B) Log Likelihood (K).

Figure S1. Locations of each of the sampled populations for the two spruce species studied here, P. asperata and P. crassifolia. Figure S2. Estimated number of clusters (K) obtained with Structure. Table S1. Nucleotide variation at 13 loci in P. asperata and P. crassifolia. Table S2. The number of segregating sites at 13 loci for P. asperata and...

Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial speciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai-Tibet Plateau...

Geographical variation in the interacting traits of plant–pollinator mutualism can lead to local adaptive differentiation. We tested Darwin's hypothesis of reciprocal selection as a key driving force for the evolution of floral traits of an alpine ginger ( Roscoea purpurea ) and proboscis length of a tabanid fly ( Philoliche longirostris ). We docu...

Hybridization and introgression are believed to play important roles in plant evolution. However, few empirical studies have been designed to clarify the ways in which these processes complicate taxonomic delimitation. Recent phylogenetic studies based on a number of different DNA fragments have indicated that Picea brachytyla in the eastern Qingha...

Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial spe-ciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai-Tibet Platea...

Species delimitation is fundamental to the basic understanding of biodiversity because of the central role that the concept of species plays in most branches of biology. However, few studies have been designed to test conflicting delineations of plant species under an integrated species concept using DNA barcodes in combination with other lines of...

Eutrema salsugineum (= Thellungiella salsuginea Brassicaceae), a species growing in highly saline habitats, is a good model for use in salt-stress research. However, its evolutionary migrations and genetic variations within and between disjunct regions from central Asia to northern China and North America remain largely unknown. We examined genetic...

It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD-psaI...

AimTo address whether climate changes have altered the distributional ranges of cold-preferring conifer species, and whether this has influenced interspecific divergence.LocationQinghai-Tibet Plateau (QTP), Asia.Methods We obtained DNA sequences at 13 nuclear loci in 229 individuals collected from 32 populations across the range of two cold-preferr...

Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using popu...

Abstract We used the Allium przewalskianum diploid–tetraploid complex on the Qinghai-Tibetan Plateau (QTP) as a model to examine how this complex responded to the Quaternary climatic oscillations, and whether multiple autopolyploidizations have occurred. We sequenced five chloroplast DNA (cpDNA) fragments (accD-psaI, trnH-psbA, trnL-trnF, trnS-trnG...

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from differen...

Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai-Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and...

Background and Aims Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of sp...

A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their r...

Abstract Phylogeography has been one major focus of evolutionary biology in recent years, with many important advances in Chinese species. In this issue, we collected 11 phylogeographic studies of plants by Chinese laboratories. We further synthesized the main findings and patterns emerging from these and previous phylogeographic studies in China a...

A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals...

Background: Most empirical studies to date have suggested that alpine plants in the central Qinghai-Tibetan Plateau (QTP) originated from the south-eastern QTP. However, previous phylogeographcial analysis of Potentilla fruticosa suggested that it diversified in the central QTP, which has also been assumed to have been a glacial refugium, and expan...

We used the Allium przewalskianum diploid-tetraploid complex on the Qinghai-Tibetan Plateau (QTP) as a model to examine how this complex responded to the Quaternary climatic oscillations, and whether multiple autopolyploidizations have occurred. We sequenced five chloroplast DNA (cpDNA) fragments (accD-psaI, trnH-psbA, trnL-trnF, trnS-trnG and rpl1...