Chi-Ming Hu

Molecular phylogeny of Lysimachia (Myrsinaceae) based on chloroplast trnL-F and nuclear ribosomal ITS sequences.

Both nuclear ribosomal ITS and chloroplast trnL-F sequences were acquired for 57 species (accessions) of Lysimachia and its close relatives, and were analyzed together with sequences retrieved from databases. The results of phylogenetic analyses based on these data (separately or combined) show that Lysimachia is paraphyletic, with the monotypic genus Glaux nested deeply inside. Previous suggestions that Anagallis and Trientalis could be ingroups of Lysimachia were not corroborated by our results. The molecular phylogenies do not support the current infrageneric divisions of Lysimachia. Subgenus Lysimachia contains at least five independent lineages. The Hawaii endemic subgenus Lysimachiopsis was shown to group with subgenera Palladia and Heterostylandra, instead of subgenus Idiophyton as previously suggested. The two North American representatives of Lysimachia, subgenus Seleucia and section Verticillatae of subgenus Lysimachia are group together as the most basal clade of the genus. Parallel and independent evolutions were inferred for morphological characters that were previously used as diagnostic criteria. Molecular phylogenies do not offer clear inferences on the overall historical biogeography of Lysimachia, but Southeast Asia origins of several clades, including the Hawaiian endemic clade and the Iberian Lysimachia ephemerum are strongly supported.

Testing DNA barcoding in closely related groups of Lysimachia L. (Myrsinaceae)

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 rbcLu2003+u2003matK 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.

Phylogeography of an alpine species Primuld secundiflora inferred from the chloroplast DNA sequence variation

The Hengduan Mountains (HM) and adjacent regions have been suggested as the important refugia of the temperate plants during the glacial stages. However, it remains unknown how the HM endemic species can respond to the climatic oscillations. In this study, we examined the chloroplast trnL-trnF and rps16 sequence variation of Primula secundiflora, a relatively common alpine perennial endemic to this region. Sequence data were obtained from 109 individuals of 11 populations covering the entire distribution range of the species. A total of 15 haplotypes were recovered and only one of them is commonly shared by three populations while the others are respectively fixed in the single population. The total diversity (HT=0.966) is high while the within-population diversity (HS=0.178) is low. Despite the high uniformity of the intraspecific morphology, an analysis of molecular variance (AMOVA) revealed a high level of genetic differentiation (97.65%) among populations. The higher NST (0.982) than GST (0.816) (P<0.05) suggested a distinctly phylogeographical pattern. Phylogenetic analyses of haplotypes identified four major clusters of the recovered haplotypes: three clades in the north, and the other one in the south. The isolated distribution of clades suggested multiple refugia of this species during the glacial stages. We failed to detect the interglacial or postglacial range expansion of this species as revealed for the other temper- ate plants. However, the low intra-population diversity suggested that most of the populations should have ex- perienced the in situ shrink-expansion cycles during the climatic oscillations. This inference was further supported by the nested clade analysis, which indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the present-day spatial distribution of haplotypes in this species. Such a special phylogeographic pattern may have resulted from a combination of both climatic oscillation and complex topology of HM.

Strong genetic differentiation of Primula sikkimensis in the East Himalaya-Hengduan Mountains.

The East Himalaya-Hengduan Mountains region is the center of diversity of the genus Primula, and P.xa0sikkimensis is one of the most common members of the genus in the region. In this study, the genetic diversity and structure of P.xa0sikkimensis populations in China were assessed using inter-simple sequence repeat (ISSR) and chloroplast microsatellite markers. The 254 individuals analyzed represented 13 populations. High levels of genetic diversity were revealed by ISSR markers. At the species level, the expected heterozygosity and Shannon’s index were 0.4032 and 0.5576, respectively. AMOVA analysis showed that 50.3% of the total genetic diversity was partitioned among populations. Three pairs of chloroplast microsatellite primers tested yielded a total of 12 size variants and 15 chloroplast haplotypes. Strong cpDNA genetic differentiation (GSTxa0=xa00.697) and evidence for phylogeographic structure were detected (NSTxa0=xa00.788, significantly higher than GST). Estimated rates of pollen-mediated gene flow are approximately 27% greater than estimated rates of seed-mediated gene flow in P. sikkimensis. Both seed and pollen dispersal, however, are limited, and gene flow among populations appears to be hindered by the patchiness of the species’ habitats and their geographic isolation. These features may have played important roles in shaping the genetic structure of P.xa0sikkimensis. A minimum-spanning tree of chloroplast DNA haplotypes was constructed, and possible glacial refugia of P.xa0sikkimensis were identified.

Population Expanding with the Phalanx Model and Lineages Split by Environmental Heterogeneity: A Case Study of Primula obconica in Subtropical China

Background Current and historical events have both affected the current distribution patterns and intraspecific divergence of plants. While numerous studies have focused on the Qinghai-Tibetan Plateau (QTP), the impacts of such events on the flora of subtropical China remain poorly understood. Subtropical China is famous for its highly complex topography and the limited impact from glaciation during the Pleistocene; this may have resulted in a different genetic legacy for species in this region compared to fully glaciated areas. Methodology/Principal Findings We used plastid and nuclear DNA sequence data and distribution modeling to analyze the divergence patterns and demographic history of Primula obconica Hance, a widespread herbaceous montane species in subtropical China. The phylogenetic analysis revealed two major lineages (lineage A and lineage B), representing a west-east split into the Yunnan and Eastern groups, and the Sichuan and Central groups, respectively. The Eastern and Central groups comprised relatively new derived haplotypes. Nested Clade Analysis and Bayesian Skyline Plot analyses both indicated that P. obconica mainly experienced a gradual expansion of populations. In addition, the simulated distribution of P. obconica during the Last Glacial Maximum was slightly larger than its present-day distribution. Conclusion/Significance Our results are the first to identify a west-east migration of P. obconica. The gradual expansion pattern and a larger potential distribution range in cold periods detected for P. obconica indicate that the population expansion of this species is consistent with the phalanx model. In addition, the current patterns of genetic differentiation have persisted as a result of the extensive environmental heterogeneity that exists in subtropical China.

DNA Barcoding Evaluation and Its Taxonomic Implications in the Species-Rich Genus Primula L. in China

The genus Primula is extremely diverse in the east Himalaya-Hengduan Mountains (HHM) in China as a result of rapid radiation. In order to overcome the difficulty of morphological classification of this genus, we surveyed three plastid regions (rbcL, matK, and trnH-psbA) and two nuclear markers (ITS and ITS2) from 227 accessions representing 66 Primula species across 18 sections, to assess their discriminatory power as barcodes. We found that ITS alone or combined with plastid regions showed the best discrimination across different infrageneric ranks and at species level. We suggest rbcL + matK + ITS as the first choice at present to barcode Primula plants. Although the present barcoding combination performed poorly in many closely related species of Primula, it still provided many new insights into current Primula taxonomy, such as the underlying presence of cryptic species, and several potential improper taxonomic treatments. DNA barcoding is one useful technique in the integrative taxonomy of the genus Primula, but it still requires further efforts to improve its effectiveness in some taxonomically challenging groups.

Primula dejuniana (Primulaceae), a New Species from Sichuan, China

Primula dejuniana G. Hao, C.M. Hu & Y. Xu sp. nova (Primulaceae) is described and illustrated from Sichuan, China. In general morphology it is clearly related to the section Petiolares subsection Davidii, which is characterized by firmly papery or leathery leaves, with veins impressed adaxially, often prominently raised and alveolate abaxially. The new species is similar to P. davidii in the indumentum and to P. tenuituba in the slender long corolla tube, but can be easily distinguished from all other species in this subsection by its leaves with an acute-apiculate apex and a sharp dentate margin.

Primula scopulicola (Primulaceae), a new species from Sichuan, southwestern China

Primula scopulicola G. Hao, C.M. Hu & Y. Xu sp. nova (Primulaceae) is described and illustrated from Sichuan, China. From general morphology it is clearly allied to the section Monocarpicae, which is characterized by the presence of multicellular hairs, distinctly petiolate leaves, a campanulate calyx, and a globose or cylindrical capsule dehiscing by valves. Primula scopulicola is similar to P. lithophila, but can be distinguished by having smaller flowers, with calyx splitting almost to the base, and the capsule being globose rather than cylindrical. It also resembles P. cavaleriei, but can be readily separated by its calyx splitting near to the base, and by the shorter petioles.

Primula anthemifolia (Primulaceae), a New Species from Sichuan, China

Primula anthemifolia G. Hao, C.M. Hu & Yuan Xu sp. nova (Primulaceae) from Sichuan, China, is described and illustrated. It is highly distinctive, with rounded pinnatisect inner leaves accompanied by subcapitate umbels, which is unique in the genus. In key morphological features it is similar to sect. Aleuritia subsect. Glabra, which is characterized by a dwarf stature, compact head-like umbels, and a calyx that equals the corolla-tube and has oblong lobes.

Primula pelargoniifolia (Primulaceae), a New Species from Chongqing, China

Primula pelargoniifolia G. Hao, C.M. Hu & Z.Y. Liu sp. nova (Primulaceae) is described from Chongqing, China, and illustrated. In general morphology it is most similar to the species in Primula section Cortusoides, which are characterized by lack of farina, subrounded leaf blade with a crenate-lobulate margin and a deeply cordate base, and by narrowly campanulate calyx that is not accrescent after anthesis. Superficially P. pelargoniifolia resembles P. heucheriifolia, but differs from it by having yellow flowers in 2–4 superimposed umbels on the scape.