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资助项目
GST, P < 0.05) were exhibited by this species. The SAMOVA revealed seven diverging groups of related chlorotypes, six of them had distinct nonoverlapping geographical ranges: one in the northeast comprising 10 populations, a second with a southeast distribution comprising 22 populations, and the remaning four groups comprising 15 populations located in the west part of the species’ range along different river valleys. The genetic clustering of populations into three regions was also supported by analysis of molecular variance, which showed that most genetic variation (82.43%) was found among these three regions. Two clusters were distinguished by both phylogenetic analysis and genealogical analysis of chlorotypes, one consisting of chlorotypes from the western region and the second consisting of those from the eastern region. Significant genetic differences between the two regions might be attributed to vicariance and restricted gene flow, and this vicariance could be explained by the physical environmental heterogeneity on each side of the Tanaka-Kaiyong Line. Following the uplift of the Tibetan Plateau, the reorganization of the major river drainages was primarily caused by river separation and capture events. These historical events could change the distribution of S. davidii from fragmented to continuous (Upper/Lower Jinshajiang and Yalongjiang/Daduhe), and from continuous to fragmented (Nujiang and Jinshajiang/Honghe). However, spatial and temporal patterns of phylogeographic divergence are strongly associated with historical disjunction rather than modern drainage connections. Moreover, the following north-south split in the eastern region and effective isolation with their genetic diversity were essentially modelled by genetic drift. The higher chlorotype richness and genetic divergence for populations in western region compared with other two regions suggests that there were multipe refugia or in situ survival of S. davidii in the Himalayan-Hengduan Mountain region. Fixation of chlorotypes in the northeastern region and near fixation in the southeastern region suggest a recent colonization of these areas. We further found that this species underwent past range expansion around 37-303 thousand years ago (kya). The southeastern populations likely experienced a demographic expansion via unidirectional gene flow along rivers, while northeastern populations underwent a more northward expansion, both from initial populations (s) (21, 22, 23) preserved on eastern refugia (Jinshajiang). This process might have been accompanied with a series of founder effects or bottlenecks making populations genetically impoverished. 3. Phylogeographic analysisbased on nuclear sequence，We sequenced the nuclear (ncpGS) region in all populations sampled, recovering 23 nuclear haplotypes. Compared to cpDNA, both NST (0.470) and GST (0.338) were relatively lower, but NST was also significantly larger than GST. 37.10% of the total variation was distributed among regions which was much lower than that shown by chlorotypes. Thus, more extensive distribution of nuclear haplotypes was exhibited across the geographical range instead of the strong population subdivision observed in chlorotypes. Similarly to the chloroplast data, we found that genetic differentiation of nDNA was positively correlated with the geographical distance, but the increase in the geographical distance between populations did not increase the genetic differentiation of nDNA as rapidly as that of cpDNA. These contrasting levels between the chloroplast and nuclear genomes of S. davidii are likely due to limited gene flow of cpDNA by seeds vs. the extensive gene flow of nDNA by wind-mediated pollen in the population history. We also determined from nuclear markers that haplotype diversity was reduced in the southeastern and northeastern regions due to the loss of rare haplotypes in western region. This reduction of gene diversity is also a signature of founder events or recent bottleneck during post-glacial colonization. However, nuclear diversity within populations remains high. This provides evidence that regionally pollen flow might be sufficiently high to blur the genetic identity of founder populations over a reasonably large spatial scale.3. Relationships among three varieties，The phylogenetic analysis identified two phylogroups of chlorotypes, corresponding to S. davidii var. davidii and var. chuansinesis. The former was distinguished by the abscence of predonminant nuclear haplotype H1 of the latter. The monophyletic group of chlorotypes in var. davidii and var. liangshanesis showed their relatively close relationship. And their genetic divergence from the third variety appears to be relative to their slight morphological difference in leaf size and the divergent environmental niche spaces they occupy. Thus, the observed differences in morphological characters between var. chuansinesis and other two varieties can be explained by the seed dispersal limitation illustrated above (as inferred by geographical separation) and by environmental heterogeneity (as inferred by precipitation or elevation) or by a combination of both. After all, the geological changes, drainage reorganization, and floristic differences following the Himalayan uplift have been suggested to affect the genetic structure of S. davidii. These results provide new insights into the phylogeographic pattern of plants in China. In addition, the unique population genetic structure found in S. davidii has provided important insights into the evolutionary history of this species. The genetic profile uncovered in this study is also critical for its conservation management. Our study has uncovered the existence of at least two ‘evolutionary significant units’ independent units within S. davidii, corresponding to var. davidii from eastern region and var. chuansinensis from western region. The conservation efforts should first focus on most western populations and on the southeastern ones exhibiting high levels of genetic diversity, while the genetically homogeneous northeastern populations located in the degraded Loess Plateau should require much greater conservation 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Taxus wallichiana complex represents an old relict conifer lineage that survived through the Tertiary. It is currently distributed in the mountain forests in South and Southwest China south of the Qinling Mountains. In the present study, we explored phylogeography of the complex by using two chloroplast DNA regions, one nuclear ribosomal DNA spacer region and eight microsatellite (SSR) loci. The main conclusions can be summarized as follows:1. Phylogeographic pattern based on chloroplast haplotypes，There were 11 cpDNA haplotypes identified in the T. wallichiana complex The complex showed a high level of genetic diversity and obvious genetic differentiation. The 44 sampled populations showed obvious genetic structure, which could be divided into five groups, namely the Huanan group, the Daba group, the Emei group, the Yunnan group and the Qinling group. There was extremely high genetic differentiation among groups, but not significant within group. The divergence times of the five lineages, estimated using average mutation rates of trnL-trnF, fell in the Pliocene. 2. Phylogeographic patterns based on ITS sequences，These included 38 unique ‘haplotypes’ based on ITS data. Their analysis showed that the T. wallichiana complex possessed a high genetic diversity. These populations could be divided into four groups, namely the Huanan group, the Daba/Emei group, the Yunnan group and the Qinling group. Based on all results, it appears that the major lineages constituting the T. wallichiana complex have arisen before Quaternary glaciation cycles, and may have survived isolated in different refugia. During interglacial periods some lineages appear to have come in contact and hybridizedbut other lineages merged forming populations with mixed haplotypes without signs of hybridization. The present-day phylogeographical distribution pattern of the T. wallichiana complex might thus be the result of repeated expansion / contractions of populations during interglacial / glacial cycles.3. Population genetic analysis using microsatellite (SSR) markers，Eight SSR loci were used for population genetic analysis on the T. wallichiana complex. A lower level of genetic diversity at the population level and high genetic differentiation among population was detected. The results of structure analysis were similar to those on the ITS data, dividing the populations into four groups (lineages). According to the results here, it was deduced that each of the 4 lineages of the T. wallichiana complex may possessed respective glacial refugia, and some lineages (such as the Qinling and Huanan lineage) might have survived in multiple refugia in the Quaternay glaciations. The present distribution pattern of this complex was likely influenced by the uplift of the QTP and Quaternary glaciation.","jscount":"1","jsurl":"/simple-search?field1=all&field=dc.date.issued.year&advanced=false&query1=%25E7%25B3%25BB%25E7%25BB%259F%25E5%2585%25B3%25E7%25B3%25BB&&fq=dc.project.title_filter%3AThe%5C+Taxus%5C+wallichiana%5C+complex%5C+represents%5C+an%5C+old%5C+relict%5C+conifer%5C+lineage%5C+that%5C+survived%5C+through%5C+the%5C+Tertiary.%5C+It%5C+is%5C+currently%5C+distributed%5C+in%5C+the%5C+mountain%5C+forests%5C+in%5C+South%5C+and%5C+Southwest%5C+China%5C+south%5C+of%5C+the%5C+Qinling%5C+Mountains.%C2%A0In%5C+the%5C+present%5C+study%2C%5C+we%5C+explored%5C+phylogeography%5C+of%5C+the%5C+complex%5C+by%5C+using%5C+two%5C+chloroplast%5C+DNA%5C+regions%2C%5C+one%5C+nuclear%5C+ribosomal%5C+DNA%5C+spacer%5C+region%5C+and%5C+eight%5C+microsatellite%5C+%5C%28SSR%5C%29%5C+loci.%5C+The%5C+main%5C+conclusions%5C+can%5C+be%5C+summarized%5C+as%5C+follows%5C%3A1.%5C+Phylogeographic%5C+pattern%5C+based%5C+on%5C+chloroplast%5C+haplotypes%EF%BC%8CThere%5C+were%5C+11%5C+cpDNA%5C+haplotypes%5C+identified%5C+in%5C+the%5C+T.%5C+wallichiana%5C+complex%5C+The%5C+complex%5C+showed%5C+a%5C+high%5C+level%5C+of%5C+genetic%5C+diversity%5C+and%5C+obvious%5C+genetic%5C+differentiation.%5C+The%5C+44%5C+sampled%5C+populations%5C+showed%5C+obvious%5C+genetic%5C+structure%2C%5C+which%5C+could%5C+be%5C+divided%5C+into%5C+five%5C+groups%2C%5C+namely%5C+the%5C+Huanan%5C+group%2C%5C+the%5C+Daba%5C+group%2C%5C+the%5C+Emei%5C+group%2C%5C+the%5C+Yunnan%5C+group%5C+and%5C+the%5C+Qinling%5C+group.%5C+There%5C+was%5C+extremely%5C+high%5C+genetic%5C+differentiation%5C+among%5C+groups%2C%5C+but%5C+not%5C+significant%5C+within%5C+group.%5C+The%5C+divergence%5C+times%5C+of%5C+the%5C+five%5C+lineages%2C%5C+estimated%5C+using%5C+average%5C+mutation%5C+rates%5C+of%5C+trnL%5C-trnF%2C%5C+fell%5C+in%5C+the%5C+Pliocene.%C2%A02.%5C+Phylogeographic%5C+patterns%5C+based%5C+on%5C+ITS%5C+sequences%EF%BC%8CThese%5C+included%5C+38%5C+unique%5C+%E2%80%98haplotypes%E2%80%99%5C+based%5C+on%5C+ITS%5C+data.%5C+Their%5C+analysis%5C+showed%5C+that%5C+the%5C+T.%5C+wallichiana%5C+complex%5C+possessed%5C+a%5C+high%5C+genetic%5C+diversity.%C2%A0These%5C+populations%5C+could%5C+be%5C+divided%5C+into%5C+four%5C+groups%2C%5C+namely%5C+the%5C+Huanan%5C+group%2C%5C+the%5C+Daba%5C%2FEmei%5C+group%2C%5C+the%5C+Yunnan%5C+group%5C+and%5C+the%5C+Qinling%5C+group.%5C+Based%5C+on%5C+all%5C+results%2C%5C+it%5C+appears%5C+that%5C+the%5C+major%5C+lineages%5C+constituting%5C+the%5C+T.%5C+wallichiana%5C+complex%5C+have%5C+arisen%5C+before%5C+Quaternary%5C+glaciation%5C+cycles%2C%5C+and%5C+may%5C+have%5C+survived%5C+isolated%5C+in%5C+different%5C+refugia.%5C+During%5C+interglacial%5C+periods%5C+some%5C+lineages%5C+appear%5C+to%5C+have%5C+come%5C+in%5C+contact%5C+and%5C+hybridizedbut%5C+other%5C+lineages%5C+merged%5C+forming%5C+populations%5C+with%5C+mixed%5C+haplotypes%5C+without%5C+signs%5C+of%5C+hybridization.%5C+The%5C+present%5C-day%5C+phylogeographical%5C+distribution%5C+pattern%5C+of%5C+the%5C+T.%5C+wallichiana%5C+complex%5C+might%5C+thus%5C+be%5C+the%5C+result%5C+of%5C+repeated%5C+expansion%5C+%5C%2F%5C+contractions%5C+of%5C+populations%5C+during%5C+interglacial%5C+%5C%2F%5C+glacial%5C+cycles.3.%5C+Population%5C+genetic%5C+analysis%5C+using%5C+microsatellite%5C+%5C%28SSR%5C%29%5C+markers%EF%BC%8CEight%5C+SSR%5C+loci%5C+were%5C+used%5C+for%5C+population%5C+genetic%5C+analysis%5C+on%5C+the%5C+T.%5C+wallichiana%5C+complex.%5C+A%5C+lower%5C+level%5C+of%5C+genetic%5C+diversity%5C+at%5C+the%5C+population%5C+level%5C+and%5C+high%5C+genetic%5C+differentiation%5C+among%5C+population%5C+was%5C+detected.%5C+The%5C+results%5C+of%5C+structure%5C+analysis%5C+were%5C+similar%5C+to%5C+those%5C+on%5C+the%5C+ITS%5C+data%2C%5C+dividing%5C+the%5C+populations%5C+into%5C+four%5C+groups%5C+%5C%28lineages%5C%29.%C2%A0According%5C+to%5C+the%5C+results%5C+here%2C%5C+it%5C+was%5C+deduced%5C+that%5C+each%5C+of%5C+the%5C+4%5C+lineages%5C+of%5C+the%5C+T.%5C+wallichiana%5C+complex%5C+may%5C+possessed%5C+respective%5C+glacial%5C+refugia%2C%5C+and%5C+some%5C+lineages%5C+%5C%28such%5C+as%5C+the%5C+Qinling%5C+and%5C+Huanan%5C+lineage%5C%29%5C+might%5C+have%5C+survived%5C+in%5C+multiple%5C+refugia%5C+in%5C+the%5C+Quaternay%5C+glaciations.%5C+The%5C+present%5C+distribution%5C+pattern%5C+of%5C+this%5C+complex%5C+was%5C+likely%5C+influenced%5C+by%5C+the%5C+uplift%5C+of%5C+the%5C+QTP%5C+and%5C+Quaternary%5C+glaciation."},{"jsname":"The Xianfeng flora and its palaeoclimte were studied using three quantitative methods. The vegetation and climatic change in Yunnan were also discussed in this paper. The results are summarized as follows:1） 34 species belonging to 9 families, 21 genera were identified in Xianfeng flora. The dominant families are Fagaceae and Lauraceae. Most genera are tropic and subtropic distribution. Consequently, Xianfeng flora is a typical subtropic flora dominanted by Fagaceae and Lauraceae.2）Two new coniferous species were identified, Pinus prekesiya and Tsuga miodumosa. P. prekesiya sp. nov., which belongs to subsection Pinus of subgenus Pinus shows a combination of characters of P. kesiya and P. yunnanensis, but has a closer affinity with P. kesiya which distributes in the humid region of Yunnan and therefore suggests a more humid climate in central Yunnan during the late Miocene than today. The general cooling trend during the late Neogene and topographic change due to the dramatic Tibetan uplift might have cause a vicariance origin of P. kesiya and P. yunnanensis from the ancestral P. prekesiya. Tsuga miodumosa shows a closest affinity with T. dumosa and might represent the ancestral stock of T. dumosa. The discovery of the Tsuga cone confirmed the presence of Tsuga in the Miocene of southwestern China and represents the earliest Tsuga megafossil record in China. The new species provides fossil evidence to support molecular phylogeny study that T. dumosa might be differentiated in the Miocene. It also support the hypothesis that diversification of the genus occurred mainly during Miocene and Pliocene time as global climate cooled and new habitats formed in response to major orogenic events.3）The MATs results from three methods (CA: 17.2-18.0°C；CLAMP3B: 15.7±1.33°C；LMA: 17.2±1.6°C) are higher than present. This indicates that the climate at late Miocene is warmer than today. The MAPs from CA and CLAMP are 1206-1537.4mm and 1297.0±184.7mm respectively, which are higher than today (1003.2mm) obviously. This indicates that the climate is more humid in late Miocene. The differences between precipitation in humid season and dry season suggest the existence of seasonality，but not so strong as today. The palaeoelevation was reconstructed using CA method; the result indicates a lower elevation (1330-1500m) of Xianfeng in late Miocene compared to today.4) The palaeoenvirmental change was discussed based on the comparisons of fossil records and paleoclimate constructions. The results show that, at late Miocene, most floras represented ever-green forests dominanted by Fagaceae and Lauraceae etc. The climate of Yunnan in Miocene was warmer and more humid than today. At Pliocene age, the vegetation type in West Yunnan is still typical ever-green forest, while in the Sanying flora, the species adapt to cold environment like Quercus sect. Heterobalnus increased greatly.5) Two monsoon sensitivity indices were used to illustrate the change of sensitivity of monsoon climate. The results suggest lower seasonality and monsoon sensitivity, especially the winter monsoon sensitivity during late Miocene.","jscount":"1","jsurl":"/simple-search?field1=all&field=dc.date.issued.year&advanced=false&query1=%25E7%25B3%25BB%25E7%25BB%259F%25E5%2585%25B3%25E7%25B3%25BB&&fq=dc.project.title_filter%3AThe%5C+Xianfeng%5C+flora%5C+and%5C+its%5C+palaeoclimte%5C+were%5C+studied%5C+using%5C+three%5C+quantitative%5C+methods.%5C+The%5C+vegetation%5C+and%5C+climatic%5C+change%5C+in%5C+Yunnan%5C+were%5C+also%5C+discussed%5C+in%5C+this%5C+paper.%5C+The%5C+results%5C+are%5C+summarized%5C+as%5C+follows%5C%3A1%EF%BC%89%5C+34%5C+species%5C+belonging%5C+to%5C+9%5C+families%2C%5C+21%5C+genera%5C+were%5C+identified%5C+in%5C+Xianfeng%5C+flora.%5C+The%5C+dominant%5C+families%5C+are%5C+Fagaceae%5C+and%5C+Lauraceae.%5C+Most%5C+genera%5C+are%5C+tropic%5C+and%5C+subtropic%5C+distribution.%5C+Consequently%2C%5C+Xianfeng%5C+flora%5C+is%5C+a%5C+typical%5C+subtropic%5C+flora%5C+dominanted%5C+by%5C+Fagaceae%5C+and%5C+Lauraceae.2%EF%BC%89Two%5C+new%5C+coniferous%5C+species%5C+were%5C+identified%2C%5C+Pinus%5C+prekesiya%5C+and%5C+Tsuga%5C+miodumosa.%5C+P.%5C+prekesiya%5C+sp.%5C+nov.%2C%5C+which%5C+belongs%5C+to%5C+subsection%5C+Pinus%5C+of%5C+subgenus%5C+Pinus%5C+shows%5C+a%5C+combination%5C+of%5C+characters%5C+of%5C+P.%5C+kesiya%5C+and%5C+P.%5C+yunnanensis%2C%5C+but%5C+has%5C+a%5C+closer%5C+affinity%5C+with%5C+P.%5C+kesiya%5C+which%5C+distributes%5C+in%5C+the%5C+humid%5C+region%5C+of%5C+Yunnan%5C+and%5C+therefore%5C+suggests%5C+a%5C+more%5C+humid%5C+climate%5C+in%5C+central%5C+Yunnan%5C+during%5C+the%5C+late%5C+Miocene%5C+than%5C+today.%5C+The%5C+general%5C+cooling%5C+trend%5C+during%5C+the%5C+late%5C+Neogene%5C+and%5C+topographic%5C+change%5C+due%5C+to%5C+the%5C+dramatic%5C+Tibetan%5C+uplift%5C+might%5C+have%5C+cause%5C+a%5C+vicariance%5C+origin%5C+of%5C+P.%5C+kesiya%5C+and%5C+P.%5C+yunnanensis%5C+from%5C+the%5C+ancestral%5C+P.%5C+prekesiya.%5C+Tsuga%5C+miodumosa%5C+shows%5C+a%5C+closest%5C+affinity%5C+with%5C+T.%5C+dumosa%5C+and%5C+might%5C+represent%5C+the%5C+ancestral%5C+stock%5C+of%5C+T.%5C+dumosa.%5C+The%5C+discovery%5C+of%5C+the%5C+Tsuga%5C+cone%5C+confirmed%5C+the%5C+presence%5C+of%5C+Tsuga%5C+in%5C+the%5C+Miocene%5C+of%5C+southwestern%5C+China%5C+and%5C+represents%5C+the%5C+earliest%5C+Tsuga%5C+megafossil%5C+record%5C+in%5C+China.%5C+The%5C+new%5C+species%5C+provides%5C+fossil%5C+evidence%5C+to%5C+support%5C+molecular%5C+phylogeny%5C+study%5C+that%5C+T.%5C+dumosa%5C+might%5C+be%5C+differentiated%5C+in%5C+the%5C+Miocene.%5C+It%5C+also%5C+support%5C+the%5C+hypothesis%5C+that%5C+diversification%5C+of%5C+the%5C+genus%5C+occurred%5C+mainly%5C+during%5C+Miocene%5C+and%5C+Pliocene%5C+time%5C+as%5C+global%5C+climate%5C+cooled%5C+and%5C+new%5C+habitats%5C+formed%5C+in%5C+response%5C+to%5C+major%5C+orogenic%5C+events.3%EF%BC%89The%5C+MATs%5C+results%5C+from%5C+three%5C+methods%5C+%5C%28CA%5C%3A%5C+17.2%5C-18.0%C2%B0C%EF%BC%9BCLAMP3B%5C%3A%5C+15.7%C2%B11.33%C2%B0C%EF%BC%9BLMA%5C%3A%5C+17.2%C2%B11.6%C2%B0C%5C%29%5C+are%5C+higher%5C+than%5C+present.%5C+This%5C+indicates%5C+that%5C+the%5C+climate%5C+at%5C+late%5C+Miocene%5C+is%5C+warmer%5C+than%5C+today.%5C+The%5C+MAPs%5C+from%5C+CA%5C+and%5C+CLAMP%5C+are%5C+1206%5C-1537.4mm%5C+and%5C+1297.0%C2%B1184.7mm%5C+respectively%2C%5C+which%5C+are%5C+higher%5C+than%5C+today%5C+%5C%281003.2mm%5C%29%5C+obviously.%5C+This%5C+indicates%5C+that%5C+the%5C+climate%5C+is%5C+more%5C+humid%5C+in%5C+late%5C+Miocene.%5C+The%5C+differences%5C+between%5C+precipitation%5C+in%5C+humid%5C+season%5C+and%5C+dry%5C+season%5C+suggest%5C+the%5C+existence%5C+of%5C+seasonality%EF%BC%8Cbut%5C+not%5C+so%5C+strong%5C+as%5C+today.%5C+The%5C+palaeoelevation%5C+was%5C+reconstructed%5C+using%5C+CA%5C+method%5C%3B%5C+the%5C+result%5C+indicates%5C+a%5C+lower%5C+elevation%5C+%5C%281330%5C-1500m%5C%29%5C+of%5C+Xianfeng%5C+in%5C+late%5C+Miocene%5C+compared%5C+to%5C+today.4%5C%29%5C+The%5C+palaeoenvirmental%5C+change%5C+was%5C+discussed%5C+based%5C+on%5C+the%5C+comparisons%5C+of%5C+fossil%5C+records%5C+and%5C+paleoclimate%5C+constructions.%5C+The%5C+results%5C+show%5C+that%2C%5C+at%5C+late%5C+Miocene%2C%5C+most%5C+floras%5C+represented%5C+ever%5C-green%5C+forests%5C+dominanted%5C+by%5C+Fagaceae%5C+and%5C+Lauraceae%5C+etc.%5C+The%5C+climate%5C+of%5C+Yunnan%5C+in%5C+Miocene%5C+was%5C+warmer%5C+and%5C+more%5C+humid%5C+than%5C+today.%5C+At%5C+Pliocene%5C+age%2C%5C+the%5C+vegetation%5C+type%5C+in%5C+West%5C+Yunnan%5C+is%5C+still%5C+typical%5C+ever%5C-green%5C+forest%2C%5C+while%5C+in%5C+the%5C+Sanying%5C+flora%2C%5C+the%5C+species%5C+adapt%5C+to%5C+cold%5C+environment%5C+like%5C+Quercus%5C+sect.%5C+Heterobalnus%5C+increased%5C+greatly.5%5C%29%5C+Two%5C+monsoon%5C+sensitivity%5C+indices%5C+were%5C+used%5C+to%5C+illustrate%5C+the%5C+change%5C+of%5C+sensitivity%5C+of%5C+monsoon%5C+climate.%5C+The%5C+results%5C+suggest%5C+lower%5C+seasonality%5C+and%5C+monsoon%5C+sensitivity%2C%5C+especially%5C+the%5C+winter%5C+monsoon%5C+sensitivity%5C+during%5C+late%5C+Miocene."},{"jsname":"The origin center and diversity center of the genus Ligularia were considered to be central China and Hengduan Mountains Region (HMR) of China, respectively. In this research, we studied the phylogeographic pattern of L. hodgsonii and L. tongolensis, which was distributed in the origin center and diversity center, respectively. We aimed to infer the evolutionary process of Ligularia species. 1. The phylogeography of L. hodgsonii，Here, we investigated the phylogeographic history of L. hodgsonii disjunctively distributed in China and Japan. Two hundred and eighty individuals were collected from 29 natural populations, 23 located in China and 6 in Japan. A total of 19 haplotypes were identified with the combination of three chloroplast DNA (cpDNA) sequences variations (trnQ-5’rps16, trnL-rpl32 and psbA-trnH). At the species level, a high level of haplotype diversity (Hd) and total genetic diversity (HT) was detected. However, the average intrapopulation diversity (HS) was very low. Consequently, the population differentiation(NST = 0.989, GST = 0.933 ) was pronounced with a significant phylogeographic structure (NST > GST, p < 0.01). At the regional level, Chinese and Japanese L. hodgsonii had a similar estimate of genetic diversity (China: Hd = 0.847, HT = 0.869; Japan: Hd = 0.766, HT = 0.867). Populations from China and Japan possess unique sets of haplotypes, and no haplotypes were shared between the regions. Furthermore, both the phyloegenetic and network analyses recovered the haplotypes of China and Japan as two distinct clades. Thus, we suggested the disjunct distribution of L. hodgsonii in China and Japan may present the climatic vicariant relicts of the ancient widely distributed populations. After divergence, this species within each region experienced independent evolutionary process. In China, L. hodgsonii was distributed around the Sichuan Basin. This distribution range can be divided into five regions. They were Jiajin Mountain region, E’mei Mountain region, Yunnan-Guizhou Plateau region, Wushan-Wuling Mountain region and Qinling Mountain region. Twelve haplotypes were indentified within these regions. Each region had its own specific haplotypes, which had different ancestry in the network. We deduced that Chinese L. hodgsonii might survive the LGM in multiple isolated refugia around the Sichuan Basin. In Japan, L. hodgsonii was disjunctively distributed in northern Honshu and Hokkaido. Seven haplotypes were identified within this region. However, the genetic diversity in Honshu (Hd = 0.821) was much higher than that in Hokkaido (Hd = 0.513). And all haplotypes in Hokkaido were derived from Honshu. This haplotype distribution suggested that the northern Honshu could have served as refuge in Japan. Nested clade analysis (NCA) indicated multiple forces including the vicariance and long-distance dispersal affected the disjunctive distribution among populations of L. hodgsonii in Japan.2. The phylogeography of L. tongolensis，Ligularia tongolensis was distributed along the Jinshajiang watershed, Yalongjiang watershed and Wumeng Mountain. In order to deduce the demographic history of this species, we sequenced two chloroplast DNA (cpDNA) intergenic spacers (trnQ-5’rps16, trnL-rpl32) in 140 individuals from 14 populations of three groups (Jinshajiang vs. Yalongjiang vs. Wumeng) within this species range. High levels of haplotype diversity (Hd = 0.814) and total genetic diversity (HT = 0.862) were detected at the species level, based on a total oftwelve haplotypes identified. However, the intrapopulation diversity (HS = 0.349) was low, which led to the high levels of genetic divergence (GST = 0.595, NST = 0.614, FST = 0.597). In consideration of the speciation of L. tongolensis resulting from the uplifts of the Qinghai-Tibetan Plateau (QTP), we thought the present genetic structure of L. tongolensis was shaped by the fragmentation of ancestral populations during the courses of QTP uplifts. This was further supported by the absence of IBD tests (r = –0.291, p = 0.964), which suggest that the differentiation had not occurred in accordance with the isolation by distance model. The genetic differentiation in L. tongolensis appears to be associated with historical events. Meanwhile, H2 and H5, the dominant haplotypes that located on internal nodes and deviated from extinct ancestral haplotype in the network, were detected to be shared between Jinshajiang and Yalongjiang groups. We deduced that ancestral populations of this species might have had a continuous distribution range, which was then fragmented and isolated by the following tectonic events. Finally, the ancestral polymorphism, H2 and H5, were randomly allocated in Jinshajiang watershed and Yalongjiang watershed. Meanwhile, H5 was the dominant haplotype in Jinshajiang watershed; H7 was the domiant haplotype in Yalongjiang watershed and Wumeng Mountain. This haplotype distribution pattern indicated that each group might have served as a refuge for L. tongolensis during the Quaternary Glaciation. Postglacial demographic expansion was supported by unimodal mismatch distribution and star-like phylogenies, with expansion ages of 274 ka B. P. for this 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temperate woody bamboos are a morphologically diverse group with a complicated taxonomy. The Arundinaria group has an East Asia-North America disjunct distribution, which is one of those with complex taxonomy in the temperate woody bamboos. In this study, the phylogeny of the temperate woody bamboos was reconstructed based on eight non-coding regions of the chloroplast genome and nuclear gene GBSSI using large sample set (124 species in 24 genera) with an emphasis on the Arundinaria group. The monophyly of the temperate woody bamboos was resolved in all phylogenies. Ten major lineages were obtained in the chloroplast phylogeny with unresolved relationships among them; the recovered phylogeny is strongly incongruent with the classifications based on morphology at both subtribal and generic ranks; some subclades that are related to the geographic distribution were obtained in those lineages. Five lineages in the GBSSI gene phylogeny were recovered as the same in the chloroplast phylogeny, and the other lineages were incongruent with chloroplast phylogeny in some ways. The reticulate evolution caused by hybridization, introgression and lineage sorting may be an explanation for the molecular phylogenetic incongruence. Based on the facts of diverse morphology, broad distribution and molecular phylogeny, we inferred that the major clades and species within most of the clades of the temperate woody bamboos were originated during several rapid adaptive radiations. Ten putative hybrids were discussed based on molecular phylogenies, morphology and distribution. The micromorphology of the leaf epidermis under SEM (scanning electron microscope) was observed and divided into nine types; the micromorphology can provide some evidence for the bamboo taxonomy and inference of putative hybrids. Additionally, taxonomic revisions were presented for some species based on field observation and herbarium work.","jscount":"1","jsurl":"/simple-search?field1=all&field=dc.date.issued.year&advanced=false&query1=%25E7%25B3%25BB%25E7%25BB%259F%25E5%2585%25B3%25E7%25B3%25BB&&fq=dc.project.title_filter%3AThe%5C+temperate%5C+woody%5C+bamboos%5C+are%5C+a%5C+morphologically%5C+diverse%5C+group%5C+with%5C+a%5C+complicated%5C+taxonomy.%5C+The%5C+Arundinaria%5C+group%5C+has%5C+an%5C+East%5C+Asia%5C-North%5C+America%5C+disjunct%5C+distribution%2C%5C+which%5C+is%5C+one%5C+of%5C+those%5C+with%5C+complex%5C+taxonomy%5C+in%5C+the%5C+temperate%5C+woody%5C+bamboos.%5C+In%5C+this%5C+study%2C%5C+the%5C+phylogeny%5C+of%5C+the%5C+temperate%5C+woody%5C+bamboos%5C+was%5C+reconstructed%5C+based%5C+on%5C+eight%5C+non%5C-coding%5C+regions%5C+of%5C+the%5C+chloroplast%5C+genome%5C+and%5C+nuclear%5C+gene%5C+GBSSI%5C+using%5C+large%5C+sample%5C+set%5C+%5C%28124%5C+species%5C+in%5C+24%5C+genera%5C%29%5C+with%5C+an%5C+emphasis%5C+on%5C+the%5C+Arundinaria%5C+group.%5C+The%5C+monophyly%5C+of%5C+the%5C+temperate%5C+woody%5C+bamboos%5C+was%5C+resolved%5C+in%5C+all%5C+phylogenies.%5C+Ten%5C+major%5C+lineages%5C+were%5C+obtained%5C+in%5C+the%5C+chloroplast%5C+phylogeny%5C+with%5C+unresolved%5C+relationships%5C+among%5C+them%5C%3B%5C+the%5C+recovered%5C+phylogeny%5C+is%5C+strongly%5C+incongruent%5C+with%5C+the%5C+classifications%5C+based%5C+on%5C+morphology%5C+at%5C+both%5C+subtribal%5C+and%5C+generic%5C+ranks%5C%3B%5C+some%5C+subclades%5C+that%5C+are%5C+related%5C+to%5C+the%5C+geographic%5C+distribution%5C+were%5C+obtained%5C+in%5C+those%5C+lineages.%5C+Five%5C+lineages%5C+in%5C+the%5C+GBSSI%5C+gene%5C+phylogeny%5C+were%5C+recovered%5C+as%5C+the%5C+same%5C+in%5C+the%5C+chloroplast%5C+phylogeny%2C%5C+and%5C+the%5C+other%5C+lineages%5C+were%5C+incongruent%5C+with%5C+chloroplast%5C+phylogeny%5C+in%5C+some%5C+ways.%5C+The%5C+reticulate%5C+evolution%5C+caused%5C+by%5C+hybridization%2C%5C+introgression%5C+and%5C+lineage%5C+sorting%5C+may%5C+be%5C+an%5C+explanation%5C+for%5C+the%5C+molecular%5C+phylogenetic%5C+incongruence.%5C+Based%5C+on%5C+the%5C+facts%5C+of%5C+diverse%5C+morphology%2C%5C+broad%5C+distribution%5C+and%5C+molecular%5C+phylogeny%2C%5C+we%5C+inferred%5C+that%5C+the%5C+major%5C+clades%5C+and%5C+species%5C+within%5C+most%5C+of%5C+the%5C+clades%5C+of%5C+the%5C+temperate%5C+woody%5C+bamboos%5C+were%5C+originated%5C+during%5C+several%5C+rapid%5C+adaptive%5C+radiations.%5C+Ten%5C+putative%5C+hybrids%5C+were%5C+discussed%5C+based%5C+on%5C+molecular%5C+phylogenies%2C%5C+morphology%5C+and%5C+distribution.%5C+The%5C+micromorphology%5C+of%5C+the%5C+leaf%5C+epidermis%5C+under%5C+SEM%5C+%5C%28scanning%5C+electron%5C+microscope%5C%29%5C+was%5C+observed%5C+and%5C+divided%5C+into%5C+nine%5C+types%5C%3B%5C+the%5C+micromorphology%5C+can%5C+provide%5C+some%5C+evidence%5C+for%5C+the%5C+bamboo%5C+taxonomy%5C+and%5C+inference%5C+of%5C+putative%5C+hybrids.%5C+Additionally%2C%5C+taxonomic%5C+revisions%5C+were%5C+presented%5C+for%5C+some%5C+species%5C+based%5C+on%5C+field%5C+observation%5C+and%5C+herbarium%5C+work."},{"jsname":"Transposable elements (TEs) have been found to be a significant fraction of eukaryotic genomes. Moreover, they make great contributions to the structure, function and evolution of genomes as well as genes. However, some questions such as the mechanisms of retainment of TEs in the genome and their adaptive evolution have not been fully elucidated so far. In this study, the distributions of 17 TE-gene associations among Oryza species were investigated. In addition, the nucleotide diversity was analysed and neutral tests for the region flanking the TE insertions were performed. Based on the above-observed patterns, evolutionary relationships between species in the AA genome group were discussed. The main results are as follows: For each TE-gene association, PCR and electrophoresis were conducted for a total of 107 strains, belonging to different Oryza species. The patterns of each TE-gene association in different species were obtained. It is our finding that 2 associations distribute through all Oryza species. By contrast, other 15 associations were only observed in some Oryza species. On basis of the above-mentioned results, it is likely that insertion events under study occurred in their common ancestor, and then they dispersed with subsequent divergence of different AA genome species. Our datas strongly support that O. meridionalis is the most basal lineage of AA genome group, instead of O. longistaminata.For several TE-gene associations fixed in populations of ancestor, the nucleotide diversity was estimated and neutral tests for the region flanking the TE insertions between populations with and without TE insertions were performed. No significant result was obtained. It is possible that the fixation of mutations with TE insetion is a random process; alternatively, this process is attributable to nature selection. Since the fixation has finished, it is difficult to detect the signature at the sequence level.","jscount":"1","jsurl":"/simple-search?field1=all&field=dc.date.issued.year&advanced=false&query1=%25E7%25B3%25BB%25E7%25BB%259F%25E5%2585%25B3%25E7%25B3%25BB&&fq=dc.project.title_filter%3ATransposable%5C+elements%5C+%5C%28TEs%5C%29%5C+have%5C+been%5C+found%5C+to%5C+be%5C+a%5C+significant%5C+fraction%5C+of%5C+eukaryotic%5C+genomes.%5C+Moreover%2C%5C+they%5C+make%5C+great%5C+contributions%5C+to%5C+the%5C+structure%2C%5C+function%5C+and%5C+evolution%5C+of%5C+genomes%5C+as%5C+well%5C+as%5C+genes.%5C+However%2C%5C+some%5C+questions%5C+such%5C+as%5C+the%5C+mechanisms%5C+of%5C+retainment%5C+of%5C+TEs%5C+in%5C+the%5C+genome%5C+and%5C+their%5C+adaptive%5C+evolution%5C+have%5C+not%5C+been%5C+fully%5C+elucidated%5C+so%5C+far.%5C+In%5C+this%5C+study%2C%5C+the%5C+distributions%5C+of%5C+17%5C+TE%5C-gene%5C+associations%5C+among%5C+Oryza%5C+species%5C+were%5C+investigated.%5C+In%5C+addition%2C%5C+the%5C+nucleotide%5C+diversity%5C+was%5C+analysed%5C+and%5C+neutral%5C+tests%5C+for%5C+the%5C+region%5C+flanking%5C+the%5C+TE%5C+insertions%5C+were%5C+performed.%5C+Based%5C+on%5C+the%5C+above%5C-observed%5C+patterns%2C%5C+evolutionary%5C+relationships%5C+between%5C+species%5C+in%5C+the%5C+AA%5C+genome%5C+group%5C+were%5C+discussed.%5C+The%5C+main%5C+results%5C+are%5C+as%5C+follows%5C%3A%5C+For%5C+each%5C+TE%5C-gene%5C+association%2C%5C+PCR%5C+and%5C+electrophoresis%5C+were%5C+conducted%5C+for%5C+a%5C+total%5C+of%5C+107%5C+strains%2C%5C+belonging%5C+to%5C+different%5C+Oryza%5C+species.%5C+The%5C+patterns%5C+of%5C+each%5C+TE%5C-gene%5C+association%5C+in%5C+different%5C+species%5C+were%5C+obtained.%5C+It%5C+is%5C+our%5C+finding%5C+that%5C+2%5C+associations%5C+distribute%5C+through%5C+all%5C+Oryza%5C+species.%5C+By%5C+contrast%2C%5C+other%5C+15%5C+associations%5C+were%5C+only%5C+observed%5C+in%5C+some%5C+Oryza%5C+species.%5C+On%5C+basis%5C+of%5C+the%5C+above%5C-mentioned%5C+results%2C%5C+it%5C+is%5C+likely%5C+that%5C+insertion%5C+events%5C+under%5C+study%5C+occurred%5C+in%5C+their%5C+common%5C+ancestor%2C%5C+and%5C+then%5C+they%5C+dispersed%5C+with%5C+subsequent%5C+divergence%5C+of%5C+different%5C+AA%5C+genome%5C+species.%5C+Our%5C+datas%5C+strongly%5C+support%5C+that%5C+O.%5C+meridionalis%5C+is%5C+the%5C+most%5C+basal%5C+lineage%5C+of%5C+AA%5C+genome%5C+group%2C%5C+instead%5C+of%5C+O.%5C+longistaminata.For%5C+several%5C+TE%5C-gene%5C+associations%5C+fixed%5C+in%5C+populations%5C+of%5C+ancestor%2C%5C+the%5C+nucleotide%5C+diversity%5C+was%5C+estimated%5C+and%5C+neutral%5C+tests%5C+for%5C+the%5C+region%5C+flanking%5C+the%5C+TE%5C+insertions%5C+between%5C+populations%5C+with%5C+and%5C+without%5C+TE%5C+insertions%5C+were%5C+performed.%5C+No%5C+significant%5C+result%5C+was%5C+obtained.%5C+It%5C+is%5C+possible%5C+that%5C+the%5C+fixation%5C+of%5C+mutations%5C+with%5C+TE%5C+insetion%5C+is%5C+a%5C+random%5C+process%5C%3B%5C+alternatively%2C%5C+this%5C+process%5C+is%5C+attributable%5C+to%5C+nature%5C+selection.%5C+Since%5C+the%5C+fixation%5C+has%5C+finished%2C%5C+it%5C+is%5C+difficult%5C+to%5C+detect%5C+the%5C+signature%5C+at%5C+the%5C+sequence%5C+level."},{"jsname":"the combination of Rodgersia, Astilboides, Darmera, Oresitrophe, Bergenia, and Mukdenia by Soltis with the name of Darmera group was supported. The key taxonomic traits of leave arrangement and pubescence were not suppoted by molecular result, especially for taxa from Hengduan Mountains and Himalayas. Multiple sampled Rodgersia aesculifolia was not monophyly, samples from Hengduan Mountains (R. henrici = R. aesculifolia var. henrici) were nested with R. pinnata and R. sambucifolia, while samples from southeast Tibet (R. henrici = R. aesculifolia var. henrici) form a clade sister to the former taxa. Samples of R. aesculifolia from Qingling and Daba mountains (R. aesculifolia var. aesculifolia = Triditional R. asculifolia) are distinct with all the above. R. aesculifolia var. henrici is distinct from A. aesculifolia var. aesculifolia and is suggested be raised to spcies level again as Rosgersia henrici Franchet. Populations of R. henrici from western Yunnan are grouping with R. pinnata, natural hybridization are supposed to occur. Rodgersia podophylla from Korea and Japan is sister to Chinese Rodgersia. The furthermore study of infraspecific taxonomy of R. aesculifolia is suggested.The relict Rodgersia nepalensis from eastern Nepal branched first in the combined ITS and plastid tree, which is different from evidences of the traditional morphology and cytology. This might due to its narrow distribution disjuct from other species of Rodgersia, low level of gene flow and subsequent conserved genetic system. It may evolved by polyploidy, the spcecialized morphological character of R. nepalensis may be a strategy for ecological tolerance and self-protection. Our molecular phylogeny of Rodgersia is accordant with the former morphological and cytological evidences. Hybridization and polyploidy may play an important role in evolution and speciation in Rodgersia. Rodgersia may origin from northestern Asia and migrated into Hengduan mountains and Himalayas through Qingling and Daba mountains. Based on present molecular results, as well as original description papers and Type specimen, six species and two variaties were recognized in Rodgersia. Rodgersia henrici was recognized in our study, and was supported to be raised to species level again","jscount":"1","jsurl":"/simple-search?field1=all&field=dc.date.issued.year&advanced=false&query1=%25E7%25B3%25BB%25E7%25BB%259F%25E5%2585%25B3%25E7%25B3%25BB&&fq=dc.project.title_filter%3Athe%5C+combination%5C+of%5C+Rodgersia%2C%5C+Astilboides%2C%5C+Darmera%2C%5C+Oresitrophe%2C%5C+Bergenia%2C%5C+and%5C+Mukdenia%5C+by%5C+Soltis%5C+with%5C+the%5C+name%5C+of%5C+Darmera%5C+group%5C+was%5C+supported.%5C+The%5C+key%5C+taxonomic%5C+traits%5C+of%5C+leave%5C+arrangement%5C+and%5C+pubescence%5C+were%5C+not%5C+suppoted%5C+by%5C+molecular%5C+result%2C%5C+especially%5C+for%5C+taxa%5C+from%5C+Hengduan%5C+Mountains%5C+and%5C+Himalayas.%5C+Multiple%5C+sampled%5C+Rodgersia%5C+aesculifolia%5C+was%5C+not%5C+monophyly%2C%5C+samples%5C+from%5C+Hengduan%5C+Mountains%5C+%5C%28R.%5C+henrici%5C+%3D%5C+R.%5C+aesculifolia%5C+var.%5C+henrici%5C%29%5C+were%5C+nested%5C+with%5C+R.%5C+pinnata%5C+and%5C+R.%5C+sambucifolia%2C%5C+while%5C+samples%5C+from%5C+southeast%5C+Tibet%5C+%5C%28R.%5C+henrici%5C+%3D%5C+R.%5C+aesculifolia%5C+var.%5C+henrici%5C%29%5C+form%5C+a%5C+clade%5C+sister%5C+to%5C+the%5C+former%5C+taxa.%5C+Samples%5C+of%5C+R.%5C+aesculifolia%5C+from%5C+Qingling%5C+and%5C+Daba%5C+mountains%5C+%5C%28R.%5C+aesculifolia%5C+var.%5C+aesculifolia%5C+%3D%5C+Triditional%5C+R.%5C+asculifolia%5C%29%5C+are%5C+distinct%5C+with%5C+all%5C+the%5C+above.%5C+R.%5C+aesculifolia%5C+var.%5C+henrici%5C+is%5C+distinct%5C+from%5C+A.%5C+aesculifolia%5C+var.%5C+aesculifolia%5C+and%5C+is%5C+suggested%5C+be%5C+raised%5C+to%5C+spcies%5C+level%5C+again%5C+as%5C+Rosgersia%5C+henrici%5C+Franchet.%5C+Populations%5C+of%5C+R.%5C+henrici%5C+from%5C+western%5C+Yunnan%5C+are%5C+grouping%5C+with%5C+R.%5C+pinnata%2C%5C+natural%5C+hybridization%5C+are%5C+supposed%5C+to%5C+occur.%5C+Rodgersia%5C+podophylla%5C+from%5C+Korea%5C+and%5C+Japan%5C+is%5C+sister%5C+to%5C+Chinese%5C+Rodgersia.%5C+The%5C+furthermore%5C+study%5C+of%5C+infraspecific%5C+taxonomy%5C+of%5C+R.%5C+aesculifolia%5C+is%5C+suggested.The%5C+relict%5C+Rodgersia%5C+nepalensis%5C+from%5C+eastern%5C+Nepal%5C+branched%5C+first%5C+in%5C+the%5C+combined%5C+ITS%5C+and%5C+plastid%5C+tree%2C%5C+which%5C+is%5C+different%5C+from%5C+evidences%5C+of%5C+the%5C+traditional%5C+morphology%5C+and%5C+cytology.%5C+This%5C+might%5C+due%5C+to%5C+its%5C+narrow%5C+distribution%5C+disjuct%5C+from%5C+other%5C+species%5C+of%5C+Rodgersia%2C%5C+low%5C+level%5C+of%5C+gene%5C+flow%5C+and%5C+subsequent%5C+conserved%5C+genetic%5C+system.%5C+It%5C+may%5C+evolved%5C+by%5C+polyploidy%2C%5C+the%5C+spcecialized%5C+morphological%5C+character%5C+of%5C+R.%5C+nepalensis%5C+may%5C+be%5C+a%5C+strategy%5C+for%5C+ecological%5C+tolerance%5C+and%5C+self%5C-protection.%5C+Our%5C+molecular%5C+phylogeny%5C+of%5C+Rodgersia%5C+is%5C+accordant%5C+with%5C+the%5C+former%5C+morphological%5C+and%5C+cytological%5C+evidences.%5C+Hybridization%5C+and%5C+polyploidy%5C+may%5C+play%5C+an%5C+important%5C+role%5C+in%5C+evolution%5C+and%5C+speciation%5C+in%5C+Rodgersia.%5C+Rodgersia%5C+may%5C+origin%5C+from%5C+northestern%5C+Asia%5C+and%5C+migrated%5C+into%5C+Hengduan%5C+mountains%5C+and%5C+Himalayas%5C+through%5C+Qingling%5C+and%5C+Daba%5C+mountains.%5C+Based%5C+on%5C+present%5C+molecular%5C+results%2C%5C+as%5C+well%5C+as%5C+original%5C+description%5C+papers%5C+and%5C+Type%5C+specimen%2C%5C+six%5C+species%5C+and%5C+two%5C+variaties%5C+were%5C+recognized%5C+in%5C+Rodgersia.%5C+Rodgersia%5C+henrici%5C+was%5C+recognized%5C+in%5C+our%5C+study%2C%5C+and%5C+was%5C+supported%5C+to%5C+be%5C+raised%5C+to%5C+species%5C+level%5C+again"},{"jsname":"lastIndexed","jscount":"2024-04-20"}],"资助项目","dc.project.title_filter")'>
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