In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from ...In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from the 10 investigated populations. Moderate haplotype diversity (h = 0.66580) and low nucleotide diver- sity (π = 0.23 × 10 ?3 ) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195, π = 0.35 × 10 ?3 ) than that of Hainan–Laos (h = 0.00000, π = 0.00). A high level of genetic differentiation (94.74%) between the two regions was revealed by AMOVA. Nested clade analysis identified two major clusters of the five haplotypes, one clade in the Yunnan region and the other in Hainan–Laos. The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes. The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations. The Yunnan populations frequently contained an ancestral haplotype, and most of them harbored other descendent haplotypes. Based on the distribution pattern of haplotypes and the nested clade analysis results, the Yunnan region potentially had several refugia of this species during glacial periods, whereas the Hainan populations were probable new colonizations.展开更多
Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no relia...Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB-rbcL, trnH-psbA, trnL-F, trnS-G, atpF-H, rbcL, matK, rpoB, rpoC1, nadl, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nadl ) have very low variation rates, whereas atpB-rbcL, atpF-H, trnH-psbA, trnL-F and trnS-G show more variability. The most variable loci, atpB-rbcL and trnH-psbA, can distinguish three of the five species. Two two-locus combinations, atpB-rbcL+trnL-F and atpB-rbcL+atpF-H, can resolve all five species. We also find that identification powers of the loci are method-dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods. Key words atpB-rbcL, DNA barcode, Prunus sect. Persica, trnL-F.展开更多
Pseudocrossidium is a genus of 21 species belonging to the Pottiaceae with the highest concentration of taxa and morphological variation found in South America.To investigate the evolutionary relationships among the s...Pseudocrossidium is a genus of 21 species belonging to the Pottiaceae with the highest concentration of taxa and morphological variation found in South America.To investigate the evolutionary relationships among the species of Pseudocrossidium and other members of the Pottioideae,molecular phylogenetic reconstructions,using the nuclear ITS1-5.8S-ITS2,and the plastid atpB-rbcL,trnG,and trnL-F,has been performed because this genus has only been partially tested using molecular markers.Bayesian and maximum likelihood topologies show that the genus,as presently circumscribed,is polyphyletic.Consequently,the circumscription of Pseudocrossidium is amended and numerous taxonomic changes resulting from the molecular,morphological,and nomenclatural studies are proposed.The phylogenetic and morphologically divergent Pseudocrossidium mendozense is renamed as Gertrudiella mendozensis.Pseudocrossidium linearifolium and P.porphyreoneurum are representatives of the new genera Barbulastrum and Helicobarbula,respectively.Pseudocrossidium carinatum and P.santiagense are accommodated in a new genus Austrobarbula.Aloinella,nested in a paraphyletic Pseudocrossidium,is maintained at generic rank,apparently derived from Pseudocrossidium.Barbula integrifolia,B.riograndensis,and Tortula jaffuelii are transferred to Pseudocrossidium.The remaining species of Pseudocrossidium are maintained in this genus,pending further studies.Conflicts of the trees observed could be evidence of interspecific or intergeneric gene flow in various lineages in the Pottioideae.展开更多
Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. Th...Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. This plant is sterile and has long been considered a hybrid, possibly from two related species, B. purpurea and B. variegata. However, not much evidence based on molecular methods was available to support this hypothesis. In this study, sequences of internal transcribed spacer I (ITS1), rbcL and atpB-rbcL intergenic spacer for five Bauhinia species and two varieties of one of the species were determined and compared. There were two types of ITS1 sequences in B. blakeana, one indistinguishable from that of B. purpurea and the other one identical to that of B. variegata. This confirmed that B. blakeana was a hybrid of these two species. Chloroplast atpB-rbcL intergenic spacer sequence of B. blakeana was identical to that of B. purpurea, indicating that B. purpurea was the female parent. The hybridization event seemed to occur only recently and was a rare incident. Its occurrence was likely facilitated by interspecific pollen competition. It appeared that human efforts played a crucial role in the preservation and ubiquity of B. blakeana.展开更多
基金partially supported by grants from the National Natural Science Foundation of China (No.J0921030 No. 30870243)
摘要In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from the 10 investigated populations. Moderate haplotype diversity (h = 0.66580) and low nucleotide diver- sity (π = 0.23 × 10 ?3 ) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195, π = 0.35 × 10 ?3 ) than that of Hainan–Laos (h = 0.00000, π = 0.00). A high level of genetic differentiation (94.74%) between the two regions was revealed by AMOVA. Nested clade analysis identified two major clusters of the five haplotypes, one clade in the Yunnan region and the other in Hainan–Laos. The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes. The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations. The Yunnan populations frequently contained an ancestral haplotype, and most of them harbored other descendent haplotypes. Based on the distribution pattern of haplotypes and the nested clade analysis results, the Yunnan region potentially had several refugia of this species during glacial periods, whereas the Hainan populations were probable new colonizations.
基金supported by the Research Fund for the Large-scale Scientific Facilities of the Chinese Academy of Sciences (Grant No. 2009-LSF-GBOWS-01)
摘要Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB-rbcL, trnH-psbA, trnL-F, trnS-G, atpF-H, rbcL, matK, rpoB, rpoC1, nadl, and internal transcribed spacer [ITS]) as candidate DNA barcodes for peaches, using samples from 38 populations, covering all the species in sect. Persica. On the whole, the primers worked well in this group and sequencing difficulties were met only in the case of ITS locus. Five loci (rbcL, matK, rpoB, rpoC, and nadl ) have very low variation rates, whereas atpB-rbcL, atpF-H, trnH-psbA, trnL-F and trnS-G show more variability. The most variable loci, atpB-rbcL and trnH-psbA, can distinguish three of the five species. Two two-locus combinations, atpB-rbcL+trnL-F and atpB-rbcL+atpF-H, can resolve all five species. We also find that identification powers of the loci are method-dependent. The NeighborNet method shows higher species identification power than maximum parsimony, neighbor joining, and unweighted pair group method with arithmetic mean methods. Key words atpB-rbcL, DNA barcode, Prunus sect. Persica, trnL-F.
基金financed by the Spanish Ministerio de Ciencia e Innovacion(Project PID2019-103993GB-looco-fnanced by FEDER).
摘要Pseudocrossidium is a genus of 21 species belonging to the Pottiaceae with the highest concentration of taxa and morphological variation found in South America.To investigate the evolutionary relationships among the species of Pseudocrossidium and other members of the Pottioideae,molecular phylogenetic reconstructions,using the nuclear ITS1-5.8S-ITS2,and the plastid atpB-rbcL,trnG,and trnL-F,has been performed because this genus has only been partially tested using molecular markers.Bayesian and maximum likelihood topologies show that the genus,as presently circumscribed,is polyphyletic.Consequently,the circumscription of Pseudocrossidium is amended and numerous taxonomic changes resulting from the molecular,morphological,and nomenclatural studies are proposed.The phylogenetic and morphologically divergent Pseudocrossidium mendozense is renamed as Gertrudiella mendozensis.Pseudocrossidium linearifolium and P.porphyreoneurum are representatives of the new genera Barbulastrum and Helicobarbula,respectively.Pseudocrossidium carinatum and P.santiagense are accommodated in a new genus Austrobarbula.Aloinella,nested in a paraphyletic Pseudocrossidium,is maintained at generic rank,apparently derived from Pseudocrossidium.Barbula integrifolia,B.riograndensis,and Tortula jaffuelii are transferred to Pseudocrossidium.The remaining species of Pseudocrossidium are maintained in this genus,pending further studies.Conflicts of the trees observed could be evidence of interspecific or intergeneric gene flow in various lineages in the Pottioideae.
基金The Chinese Academy of Sciences(KSCX2-YW-Z-0925&O92441112F)the Ministry of Education of China through its 985 and 111 projects(MUC 98503-001006&B08044)+2 种基金the National Science Foundation of China(31070288)the Japan Society for the Promotion of Science(JSPS/AP/109080)the Ministry of Science and Technology of China(2008FY110400-2-2)
基金Partially Supported by the Chinese University of Hong Kong Strategic Research Programme.
摘要Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. This plant is sterile and has long been considered a hybrid, possibly from two related species, B. purpurea and B. variegata. However, not much evidence based on molecular methods was available to support this hypothesis. In this study, sequences of internal transcribed spacer I (ITS1), rbcL and atpB-rbcL intergenic spacer for five Bauhinia species and two varieties of one of the species were determined and compared. There were two types of ITS1 sequences in B. blakeana, one indistinguishable from that of B. purpurea and the other one identical to that of B. variegata. This confirmed that B. blakeana was a hybrid of these two species. Chloroplast atpB-rbcL intergenic spacer sequence of B. blakeana was identical to that of B. purpurea, indicating that B. purpurea was the female parent. The hybridization event seemed to occur only recently and was a rare incident. Its occurrence was likely facilitated by interspecific pollen competition. It appeared that human efforts played a crucial role in the preservation and ubiquity of B. blakeana.