Chloroplast phylogeography of Dipentodon (Dipentodontaceae) in southwest China and northern Vietnam.

The evolutionary history of plants in the southeast Tibetan Plateau might be the most complicated around the world because of the area's extremely complex topography and climate induced by strong tectonic activity in recent history. In this research, we implemented a phylogeographical study using chloroplast sequences (psbA-trnH and trnQ-rps16 intergenic spacer) on Dipentodon, a monotypic or ditypic genus (D. sinicus and D. longipedicellatus) distributed in southwest China and adjacent areas including Myanmar (Burma), northeast India and northern Vietnam. A total of 257 samples from 16 populations from the southeast Tibetan Plateau (D. longipedicellatus) and the Yungui Plateau (D. sinicus) were collected. The results revealed that Dipentodon had 11 haplotypes for the two intergenic spacers, high genetic diversity (h(T) = 0.902) and high genetic differentiation (N(ST) = 0.987 and G(ST) = 0.948). amova analysis showed that the component of among-population within region/species (55.25%) was unexpectedly larger than the among-species/region component (43.69%), which indicates that there is no justification for recognizing two species in Dipentodon. Correlation of pairwise genetic and geographical distances showed that Dipentodon populations in the southeast Tibetan Plateau may have suffered more habitat fragmentation than populations in the Yungui Plateau because of the uplift of the Tibetan Plateau than populations in the Yungui Plateau have. Nested clade analysis showed that 11 haplotypes formed two 3-level, three 2-level and seven 1-level clades, with eight clades showing significant geographical association. However, clade 2-1 and 2-2 did not cluster together, although they are distributed in the same region (Yungui Plateau) and belong to the same species (D. sinicus). This led not only to incongruence between haplotype network and geographical distribution of 2-level clades, but also to paraphyly of D. sinicus to D. longipedicellatus. We concluded that the incongruence and paraphyly may result from incomplete lineage sorting during the rapid and extreme tectonic events of the Tibetan Plateau. The results reported here will no doubt provide new insights into the evolution of biodiversity on the Tibetan Plateau and adjacent areas, and a historical framework for the conservation of biodiversity in this area, including Dipentodon.

Yuan QJ ，Zhang ZY ，Peng H ，Ge S ... -  《-》

Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation.

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N(ST) = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N(ST) > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.

Zhang Q ，Chiang TY ，George M ，Liu JQ ，Abbott RJ ... -  《MOLECULAR ECOLOGY》

Chloroplast phylogeny and phylogeography of Stellera chamaejasme on the Qinghai-Tibet Plateau and in adjacent regions.

Historic events such as the uplift of Qinghai-Tibet Plateau (Q-T Plateau) and climatic oscillations in the Quaternary period greatly affected the evolution and modern distribution of Sino-Tibetan flora. Stellera chamaejasme, a perennial herb with flower color polymorphism that is distributed from the mountainous southeastern Q-T Plateau (Hengduan Mountains, H-D Mountains) to the vast platform of the Q-T Plateau and the adjacent plain of northern China, provides an excellent model to explore the effects of historic events on the origination and variation of species. In this study, we conducted a phylogenetic and phylogeographical study using three chloroplast sequences (trnT-L, trnL-F and rpL16) in 26 populations of S. chamaejasme and 12 outgroups from the Thymeleaceae. Phylogenetic analysis and molecular clock estimation revealed that the monophyletic origin of S. chamaejasme occurred ca. 6.5892 Ma, which is consistent with the radical environment changes caused by the rapid uplift of the Q-T Plateau ca. 7 Ma. Intra-specific differentiation of S. chamaejasme is estimated to have occurred after ca. 2.1 Ma. Twelve haplotypes were revealed from combined trnL-F and rpL16 sequences. High genetic diversity (h(T)=0.834) and population differentiation (N(ST)=0.997 and G(ST)=0.982) imply restricted gene flow among populations and significant geographical or environmental isolation. All populations from the vast plain of northern China were dominated by one haplotype (H1), and the same haplotype was fixed in most populations from the high elevation platform of the western and northern Q-T Plateau. In contrast, the majority of the haplotypes were found in the relatively narrow area of the H-D Mountains, in the southeastern distribution of S. chamaejasme. The contrasting haplotype distribution patterns suggested that the H-D Mountains were either a refugium for S. chamaejasme during the Quaternary climatic oscillations or a diversification center of this species. The present wide distribution of this species on the Q-T Plateau platform and in northern China is likely to have resulted from a rapid post-glacial population expansion from the southeastern refugium involving founder effects, facilitated by the adjacent geographic range with a similar grassland habitat.

Zhang YH ，Volis S ，Sun H 《-》

Chloroplast DNA phylogeography of Clintoniaudensis Trautv. & Mey. (Liliaceae) in East Asia.

In this paper, we report the phylogeographic history of Clintoniaudensis Trautv. & Mey. (Liliaceae) inferred from two types of chloroplast DNA markers, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequences. Eighty samples were collected from 20 natural populations, 19 located in China and one in Japan, across the entire range of the species in East Asia. High genetic diversity (h(T)(PCR-RFLP)=0.972, h(T)(sequencing)=0.874) and significant differentiation (N(ST)(PCR-RFLP)=0.893, N(ST)(sequencing)=0.988 and G(ST)(PCR-RFLP)=0.777, G(ST)(sequencing)=0.978) were detected at the species level. These findings are consistent with a scenario of clonal reproduction and locally restricted gene exchange. The level of diversity of tetraploid populations was slightly greater than that of diploid populations. Significant molecular variation was found between tetraploids and diploids. Tetraploids may be autopolyploids and may have formed repeatedly in different locations. At least three regions of origin could be recognized. Twenty-six distinct haplotypes were identified. Haplotype frequency distributions were strongly skewed, with most haplotypes (n=25) represented by only one sample each and thus restricted to a single population. Non-overlapping distributions of cpDNA haplotypes and strong genetic differentiation among populations and/or different ploid level were consistent with the findings of a nested clade analysis, which inferred long-distance colonization as the major process influencing the spatial haplotype distribution of this species. Nested clade analysis showed that the 26 haplotypes formed two 3-step, four 2-step and eleven 1-step clades, with twelve clades showing significant geographical associations. Higher N(ST) than G(ST) (P<0.05) suggested a distinct phylogeographical pattern. Based on mismatch distribution analysis and neutrality tests, we found no evidence of population expansion in the species. Our analyses indicate that the history of C.udensis involved both long-distance migration and the tectonic events of Mountains in East Asia.

Wang YL ，Li X ，Guo J ，Guo ZG ，Li SF ，Zhao GF ... -  《-》

Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change.

The Qinghai-Tibetan Plateau (QTP) is thought to be more strongly affected by the Quaternary glaciations than most other regions of the same latitude. It would be of great interest to investigate the population genetic structure of organisms distributed on the platform and its correlation with the Quaternary climatic oscillations. Here we used the chloroplast (cp)DNA trnT-trnF sequence to study genetic variation and phylogeography of Pedicularis longiflora, an alpine herb with extensive distribution on the QTP. Based on a range-wide sampling comprising 41 populations and 910 individuals, we detected 30 cpDNA haplotypes that were divided into five clades by phylogenetic and network analyses and a strong phylogeographical structure. All haplotypes but one in the three basal clades occur exclusively in the southeast QTP, whereas haplotypes in the young clade V occupy almost the whole species range. In particular, the young haplotype H18 occurs in 420 individuals, even at a frequency of 100% in some QTP platform populations and the Altai population. The haplotype distribution pattern, together with molecular clock estimation and mismatch distribution analysis, suggests that the southeast QTP was either a refuge for P. longiflora during the Quaternary climatic change or is the place of origin of the species. The present wide distribution of the species on the QTP platform has resulted from recent population expansions which could be dated back to 120,000-17,000 years ago, a period mostly before the last glacial maximum. The possible relationships among geographic genetic structure, climatic change and species diversification in Pedicularis are also discussed.

Yang FS ，Li YF ，Ding X ，Wang XQ ... -  《-》