Tricyclization of an Epoxypolyene Utilizing Zeolites as Next-Generation Biomimetic Cyclization Promoters: Evidence of Surface and Pore Selectivity in the Cyclization Process^†

A new approach for the biomimetic polyene cyclization of epoxyolefins is demonstrated by the zeolite-promoted tricyclization of 1. Reaction of 1 with a variety of zeolitic materials, including Zeolite A, Mordenite, Faujasite, and ZSM-5, yielded variable amounts of cyclic and acyclic epoxide-rearranged materials. Small-pore Zeolite A, in either the Na or Li form, caused the exclusive formation of ketone 3, while both H−Mordenite and H−ZSM-5 were sufficiently reactive to provide tricyclic products in modest yields. Low recovery of polyene 1 was observed when larger-pore zeolites of type Beta and H−Faujasite were utilized as cyclization promoters, suggesting that decomposition products had been included within the zeolite cavity. Dramatic improvement in reaction selectivity was achieved after surface dealumination of H−ZSM-5, which gave 52% (isolated yield) of tricycle 2. Compared to the Lewis acid cyclization of 1 by Ti(OiPr)Cl3 or MeAlCl2, the reaction is highly stereoselective, producing the all-trans tricycle as the predominant product. These results, in conjunction with surface and pore deactivation studies using pyridine bases, suggest that the cyclization is initiated at the opening of the zeolite pores, with concurrent adsorption of the polyene onto the aluminosilicate surface

R scripts and input files

File contents: 1: Two BEAST input files for phylogenetic reconstructions; 2: input file, settings file and sample prob. file for BAMM analysis; 3: R script for downloading COI sequences from genbank; 4: R script for processing the 305 species tree (data extraction and pruning to genus tree); 5: R script for prepping 602 spp tree for BAMM and analyses of BAMM output files; 6: R scripts for SLOUCH analyse

Data_Sheet_2_The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini).PDF

DNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools and taxonomists will soon not have utility. Here we demonstrate that DNA-based identification is not reliable without the contributions of taxonomic experts. We use ambrosia beetles (Xyleborini), which are known for great diversity as well as global invasions and damage, as a test case. Recent xyleborine introductions have caused major economic and ecological losses, thus timely species identifications of new invaders are necessary. This need is hampered by a paucity of identification tools and a fauna that is only moderately documented. To help alleviate deficiencies in their identification, we created COI and CAD DNA barcode databases (490 and 429 specimens), representing over half of the known fauna of Southeast Asia (165/316 species). Taxonomic experts identified species based on original descriptions and type specimens. Tree, distance, and iterative methods were used to assess the identification and delimitation of species. High intra- and interspecific COI distances were observed for congeneric species and attributed to the beetle's inbreeding system. Neither of the two markers provided 100% identification success but with the neighbor-joining tree-based method, 80% of species were identified by both genes. As for species delimitation, an obvious barcode gap between intra- and interspecific differences was not observed. Correspondence between distance-based groups and morphology-based species was poor. In a demonstration of iterative taxonomy, we constructed parsimony-based phylogenies using COI and CAD sequences for two genera. Although not all clades were resolved or supported, we provided better explanations for species boundaries in light of morphological and DNA sequence differences. Confident species identifications demonstrated 10–12% COI and/or >2–3% CAD. Involvement of taxonomic experts from the start of this project was essential for the creation of a stable foundation for the DNA identification of xyleborine species. In general, their role in DNA barcoding cannot be underestimated and is further discussed.</p

Data_Sheet_1_The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini).PDF

DNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools and taxonomists will soon not have utility. Here we demonstrate that DNA-based identification is not reliable without the contributions of taxonomic experts. We use ambrosia beetles (Xyleborini), which are known for great diversity as well as global invasions and damage, as a test case. Recent xyleborine introductions have caused major economic and ecological losses, thus timely species identifications of new invaders are necessary. This need is hampered by a paucity of identification tools and a fauna that is only moderately documented. To help alleviate deficiencies in their identification, we created COI and CAD DNA barcode databases (490 and 429 specimens), representing over half of the known fauna of Southeast Asia (165/316 species). Taxonomic experts identified species based on original descriptions and type specimens. Tree, distance, and iterative methods were used to assess the identification and delimitation of species. High intra- and interspecific COI distances were observed for congeneric species and attributed to the beetle's inbreeding system. Neither of the two markers provided 100% identification success but with the neighbor-joining tree-based method, 80% of species were identified by both genes. As for species delimitation, an obvious barcode gap between intra- and interspecific differences was not observed. Correspondence between distance-based groups and morphology-based species was poor. In a demonstration of iterative taxonomy, we constructed parsimony-based phylogenies using COI and CAD sequences for two genera. Although not all clades were resolved or supported, we provided better explanations for species boundaries in light of morphological and DNA sequence differences. Confident species identifications demonstrated 10–12% COI and/or >2–3% CAD. Involvement of taxonomic experts from the start of this project was essential for the creation of a stable foundation for the DNA identification of xyleborine species. In general, their role in DNA barcoding cannot be underestimated and is further discussed.</p

Table_1_The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini).xlsx

DNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools and taxonomists will soon not have utility. Here we demonstrate that DNA-based identification is not reliable without the contributions of taxonomic experts. We use ambrosia beetles (Xyleborini), which are known for great diversity as well as global invasions and damage, as a test case. Recent xyleborine introductions have caused major economic and ecological losses, thus timely species identifications of new invaders are necessary. This need is hampered by a paucity of identification tools and a fauna that is only moderately documented. To help alleviate deficiencies in their identification, we created COI and CAD DNA barcode databases (490 and 429 specimens), representing over half of the known fauna of Southeast Asia (165/316 species). Taxonomic experts identified species based on original descriptions and type specimens. Tree, distance, and iterative methods were used to assess the identification and delimitation of species. High intra- and interspecific COI distances were observed for congeneric species and attributed to the beetle's inbreeding system. Neither of the two markers provided 100% identification success but with the neighbor-joining tree-based method, 80% of species were identified by both genes. As for species delimitation, an obvious barcode gap between intra- and interspecific differences was not observed. Correspondence between distance-based groups and morphology-based species was poor. In a demonstration of iterative taxonomy, we constructed parsimony-based phylogenies using COI and CAD sequences for two genera. Although not all clades were resolved or supported, we provided better explanations for species boundaries in light of morphological and DNA sequence differences. Confident species identifications demonstrated 10–12% COI and/or >2–3% CAD. Involvement of taxonomic experts from the start of this project was essential for the creation of a stable foundation for the DNA identification of xyleborine species. In general, their role in DNA barcoding cannot be underestimated and is further discussed.</p