What is the phylogenetic placement ofDipteronia dyeranaHenry? An example of plant species placement based on nucleotide sequences

Abstract

DNA sequence data have been widely used to evaluate species delimitations and examine infraspecific relationships. However, species placements inferred from different nucleotide sequences are frequently in conflict. As an example of plant species placement based on nucleotide sequences, the phylogenetic placement of Dipteronia dyerana Henry (Aceraceae) was analyzed in the present study. The study species included eight Acer species (from different sections of Acer ), two Dipteronia species, and two outgroup taxa. Phylogenetic trees based on five datasets ( ITS , trnL-F , trnD-trnT , psbM-trnD , and rpl16 regions) as well as their combined datasets were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Further analyses were conducted to compare the strict consensus trees based on single regions and the combination of different regions. The results revealed a significant discrepancy among the phylogenetic placements of D. dyerana , inferred from various sequences. Phylogenetic trees using MP analysis based on trnD-trnT , rpl16 , and the four chloroplast combined sequences supported the genus Dipteronia as a monophyletic group, while in the other trees D. dyerana was positioned either in parallel with D. sinensis and Acer species or within the genus Acer . In ML analysis, only rpl16 and the four chloroplast combined sequence datasets supported the genus Dipteronia as a monophyletic group. We concluded that, although significant genetic differentiation occurred between D. dyerana and D. sinensis , D. dyerana was more advanced than D. sinensis . However, whether Dipteronia is monophyletic remains to be further investigated, e.g., by using more closely related taxa and more sequences. Furthermore, in addition to internal transcribed spacer sequences, more chloroplast gene sequences should be used for phylogenetic analyses of species.

Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

“…Both the BI and ML analyses showed coincident topology based on different plastid regions (except for the SSC) and this was used to construct the phylogeny in which D. sinensis and D. dyeriana were clustered into a monophyletic clade. The phylogenetic trees based on complete chloroplast genomes and three different plastid regions in this study indicated that D. sinensis is usually in parallel with Acer but not with D. dyeriana , as was suggested in a previous study (Yang et al, 2010 ). This significant discrepancy in phylogenetic placement of D. dyeriana should be interpreted with caution.…”

“…Recently, single copy or low copy nuclear genes have been increasingly used to clarify phylogenetic relationship in some angiosperms and to determine the dynamics of speciation (Curto et al, 2012 ; Zhang N. et al, 2012 ; Du et al, 2015 ; Guo et al, 2015 ). Until now, only nrDNA and chloroplast markers have been used to probe phylogenetic relationships between Dipteronia and related genera (Yang et al, 2010 ). The large number of SCNGs developed in the present study will contribute substantially to the elucidation of phylogenetic relationships and to investigation of population demographic history in Dipteronia and Aceraceae species.…”

“…Plastid genomes have been proven to be effective in resolving difficult phylogenetic relationships (Ma et al, 2014 ; Carbonell-Caballero et al, 2015 ). In the present study, 11 complete chloroplast genomes of five taxa were used to resolve the still-debated phylogenetic position of Dipteronia species (Yang et al, 2010 ). In our analyses, all the species of Aceraceae formed a monophyletic clade with a high-resolution value and clustered with S. mukorossi (Sapindaceae) in the same clade.…”

Homoploid hybrid speciation inDoronicumL. (Asteraceae)? Morphological, karyological and molecular evidences

“…Okuyama et al 2005;McBreen & Lockhart 2006;Yang et al 2010). Depending on inheritance patterns, plastid DNA may permit to determine the direction of hybridization (McDade 1992;Schwarzbach & Rieseberg 2002;Albarouki & Peterson 2007).…”

Effects of cultivation years on effective constituent content ofFritillaria pallidifloraSchernk

“…Such measures play an result, the species has been classified as a level-3 important role in the conservation of biodiversity protected medicinal plant. In recent years, with (Ishtiaq et al 2010;Yang et al 2010;Tisdell 2011; continuous research and development of new drugs Pradhan & Badola 2012). The dry bulbs of Fritillaria derived from F. pallidiflora, its demand has increased pallidiflora Schrenk, a perennial herb belonging to the even further.…”