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DNA barcoding is a well‐established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographical regions. The arid region in northwestern China, a vast area of about 2.5 million km2, is ecologically fragile and often overlooked in biodiversity studies. In particular, DNA barcode data from the arid region in China are lacking. We develop and evaluate the efficacy of an extensive DNA barcode library for native flowering plants in the arid region of northwestern China. Plant specimens were collected, identified and vouchered for this purpose. The database utilized four DNA barcode markers, namely rbcL, matK, ITS and ITS2, for 1816 accessions (representing 890 species from 385 genera and 72 families), and consisted of 5196 barcode sequences. Individual barcodes varied in resolution rates: species‐ and genus‐level rates for rbcL, matK, ITS and ITS2 were 79.9%–51.1%/76.1%, 79.9%–67.2%/88.9%, 85.0%–72.0%/88.2% and 81.0%–67.4%/84.9%, respectively. The three‐barcode combination of rbcL + matK + ITS (RMI) revealed a higher species‐ and genus‐level resolution (75.5%/92.1%, respectively). A total of 110 plastomes were newly generated as super‐barcodes to increase species resolution for seven species‐rich genera, namely Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene and Zygophyllum. Plastomes revealed higher species resolution compared to standard DNA barcodes and their combination. We suggest future databases include super‐barcodes, especially for species‐rich and complex genera. The plant DNA barcode library in the current study provides a valuable resource for future biological investigations in the arid regions of China. [ABSTRACT FROM AUTHOR]

Summary: What causes the disparity in biodiversity among regions is a fundamental question in biogeography, ecology, and evolutionary biology. Evolutionary and biogeographic processes (speciation, extinction, dispersal) directly determine species richness patterns, and can be studied using integrative phylogenetic approaches. However, the strikingly high richness of East Asia relative to other Northern Hemisphere regions remains poorly understood from this perspective. Here, for the first time, we test two general hypotheses (older colonization time, faster diversification rate) to explain this pattern, using the plant tribe Lysimachieae (Primulaceae) as a model system. We generated a new time‐calibrated phylogeny for Lysimachieae (13 genes, 126 species), to estimate colonization times and diversification rates for each region and to test the relative importance of these two factors for explaining regional richness patterns. We find that neither time nor diversification rates alone explain richness patterns among regions in Lysimachieae. Instead, a new index that combines both factors explains global richness patterns in the group and their high East Asian biodiversity. Based on our results from Lysimachieae, we suggest that the high richness of plants in East Asia may be explained by a combination of older colonization times and faster diversification rates in this region. [ABSTRACT FROM AUTHOR]

A new species of Primulaceae, Primula persimilis G. Hao, C.M. Hu & Y. Xu, from Sichuan, China, is described and illustrated. In general morphology it is allied to the species of P. sect. Monocarpicae, characterized by the presence of multi-cellular hairs, the distinctly petiolate leaves, a campanulate calyx, and a globose or cylindrical capsule with valvate dehiscence. The new species superficially resembles P. tsiangii W.W. Smith, but can be distinguished by its white flowers, longer calyx lobes, and cylindrical capsules. [ABSTRACT FROM AUTHOR]

* Premise of the study: Microsatellite markers from Primula sikkimensis (Primulaceae) were developed for testing deep lineage divergence and speciation events. * Methods and Results: A total of 3112 microsatellites were identified from 61,755 unique reads though 454 pyrosequencing technology. Twenty-nine microsatellite loci were selected for PCR amplification and polymorphic analyses. Among the 29 tested markers, 17 microsatellite loci were further used for genotyping in three wild P. sikkimensis populations. The number of alleles varied from one to eight, and the observed heterozygosity ranged from 0.111 to 1.000. Ten simple sequence repeat loci could be successfully cross-amplified in two Primula species. The transferability values were 76.5% in P. florindae and 58.8% in P. alpicola, respectively. * Conclusions: These microsatellite markers will be valuable for testing the hypothesis of lineage divergence, genetic introgression, and cryptic speciation events between P. sikkimensis and its closely related taxa. [ABSTRACT FROM AUTHOR]

Aim Rapid and accurate species identification is the foundation for biodiversity assessment. DNA barcoding has been shown to be an effective tool to overcome the taxonomic impediment to facilitate biodiversity conservation in temperate forests. However, this tool has rarely been considered for use in tropical forests. This study aims to investigate the utility and species resolution of DNA barcoding in a subtropical region. Location The Dinghushan National Nature Reserve ( DNNR) in China. Methods A DNA barcoding database was constructed for 531 trees present in the DNNR. We used a phylogenetic method (neighbour-joining trees) and sequence similarity (all-to-all BLASTn searches) to evaluate the utility and species resolution of five DNA barcode regions ( rbcL, matK, ITS, ITS2 and trnH-psbA), both singly and in combinations of two or three region. Results The combination of rbcL + matK + ITS had the highest species resolution (94.19%). However, when considering the difficulty of sequence recoverability, rbcL + ITS2 performed best (64.64%). Species resolution for large genera containing more than two species was substantially lower than that for small genera with one and two species per genus. Local small spatial scales (1-ha quadrats) resulted in moderately improved species resolution (70.82% for rbcL + ITS2) compared to larger spatial scales (20 and 1133 ha). We document incongruent signals between nuclear and cp DNA regions and the challenges associated with barcoding large genera inherent to subtropical floras. Main conclusions This study considerably expands the global DNA barcode database for subtropical trees. Based on cost-effectiveness and the trade-off between sequence recovery and species resolution, we suggest that the rbcL + ITS2 barcode combination is an effective tool for documenting plant diversity in the DNNR. This study also sheds some light on the limitations and challenges for the application of barcoding to conservation biogeography in subtropical forests. [ABSTRACT FROM AUTHOR]

To investigate the mechanisms responsible for the high diversity in central and adjacent southwestern China, we inferred the phylogeographic history of Primula ovalifolia from chloroplast DNA data. One hundred and thirty five individuals from 13 natural populations (including one Primula tardiflora population) were analyzed. A total of 23 haplotypes were identified. Most of them were exclusive to a single population. Strong phylogeography structure was detected, with NST (0.936) significantly higher than GST (0.784). Phylogenetic analysis showed that all haplotypes were clustered into three lineages (clades I, II, and III). High genetic diversity was revealed, possibly due to the interglacial contraction and glacial expansion. The three identified lineages may have undergone different historical processes after the mid-Pleistocene, due to their early divergent time. Multiple refugia were inferred for the three lineages. Pleistocene climatic oscillations, combined with the complex local topography, were responsible for the strong phylogeographic pattern of P. ovalifolia. Our analysis supports the hypothesis that the central and adjacent southwestern region of China was an important refugium for the survival, persistence, and further speciation of most East Asia flora, which has led to high species diversity in this region. [ABSTRACT FROM AUTHOR]

The phylogeography of common and widespread species can help us to understand the history of local flora and vegetation. Here, we study the semi-evergreen shrub Rhododendron simsii Planch., which is found in most areas of current evergreen broad leaved forest in China. Two noncoding chloroplast DNA (cpDNA) regions ( rpl20-rps12 and trnL-F) and three amplified fragment length polymorphism (AFLP) primer sets (E-AAC/M-CTA, E-AGC/M-CTA and E-AGG/M-CAT) were used to examine the phylogeographic pattern in relation to past (last glacial maximum) and present distributions based on ecological niche modeling. The cpDNA data revealed four phylogeographic groups (East, South, West, and North groups) corresponding to geographic regions. Molecular dating suggests that lineage diversification within species likely occurred during the mid-to-late Pleistocene. In contrast, the four main cpDNA phylogeographic groups were not supported by the AFLP dataset. The highest likelihood of the AFLP data was obtained when samples were clustered into three groups ( K= 3). However, these groupings did not correspond to separate geographic regions supported by cpDNA data. Both mismatch distribution analysis and environmental niche modeling (ENM) indicated that multiple glacial refugia were maintained across the range of Rhododendron simsii during the last glacial maximum, contrary to the previous hypothesis that subtropical broad leaved evergreen forests were forced to retreat southward as far as 25° N. The discordance between the patterns revealed by cpDNA and AFLP data indicate that localized postglacial range expansions may facilitate extensive gene flow between the major glacial refugia. [ABSTRACT FROM AUTHOR]

Aim Our goals were: (1) to assess the population genetic structure and demographic divergence history of a bird-dispersed tree, Neolitsea sericea, endemic to East Asian land-bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc. Location Japan-Ryukyu-Taiwan Island Arc and Chinese/Korean offshore islands. Methods We applied 10 nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker ( psbA- trnH intergenic spacer) to 31 populations (397 and 326 individuals, respectively) from throughout the species' range to infer current patterns of genetic diversity and structure, and pollen-to-seed migration ratios ( r). A coalescent-based isolation-with-migration (IM) model was applied to the combined nSSR/cpDNA data set to estimate lineage divergence times and population demographic parameters. Results The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the 'Tokara Gap', a narrow ( c. 37 km wide) but deep (> 1000 m) sea-strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages to c. 0.07 Ma (90% highest posterior density interval: 0.02-0.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post-divergence gene flow between them. Main conclusions The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an 'ancient sea-barrier hypothesis' for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence of N. sericea, including not only land-bridge submergence, but also island configuration, and/or constraints on adaptation along a latitudinal temperature gradient. [ABSTRACT FROM AUTHOR]

It has been suggested that rbcL and matK are the core barcodes in plants, but they are not powerful enough to distinguish between closely related plant groups. Additional barcodes need to be evaluated to improve the level of discrimination between plant species. Because of their well-studied taxonomy and extreme diversity, we used Chinese Lysimachia (Myrsinaceae) species to test the performance of core barcodes ( rbcL and matK) and two additional candidate barcodes ( trnH- psbA and the nuclear ribosomal ITS); 97 accessions from four subgenus representing 34 putative Lysimachia species were included in this study. And many closely related species pairs in subgen. Lysimachia were covered to detect their discriminatory power. The inefficiency of rbcL and matK alone or combined in closely related plant groups was validated in this study. TrnH- psbA combined with rbcL + matK did not yet perform well in Lysimachia groups. In contrast, ITS, alone or combined with rbcL and/or matK, revealed high resolving ability in Lysimachia. We support ITS as a supplementary barcode on the basis of core barcode rbcL and matK. Besides, this study also illustrates several mistakes or underlying evolutionary events in Lysimachia detected by DNA barcoding. [ABSTRACT FROM AUTHOR]

A new species of Lysimachia (Primulaceae), L. huchimingii G. Hao & H. F. Yan from China is described and illustrated. It is morphologically compared to its most closely related species in Lysimachia subgen. Lysimachia sect. Nummularia ser. Paridiformes. [ABSTRACT FROM AUTHOR]