Fossil-calibrated penalized likelihood and Bayesian divergence time estimates indicate that the Northern Hemisphere Calycanthus and Chimonanthus diverged from each other in the mid-Miocene, while the Australian Idiospermum had already diverged by the Upper Cretaceous and likely represents a remnant of a former Gondwanan distribution of Calycanthaceae that included South America, as indicated by the occurrence of Cretaceous Calycanthaceae fossils in Brazil. This is the first time STLs have been reported from subtribe Madiinae.īased on nuclear and chloroplast sequences we resolve species relationships in Calycanthaceae and develop a biogeographic hypothesis that explains their intercontinental disjunctions and intra-continental diversification in eastern Asia. latifolia, and Layia hieracioides, previously not investigated for STLs, we found large amounts of xanthalongin derivatives. Morphology, STL data (PCA), cytometric data and DNA sequence data suggest a hybrid origin of one accession (A. parryi, with additional support from DNA sequence data and cytometric data. Moreover, sesquiterpene lactone data support subspecies classifications of A. Sesquiterpene lactone profiles were found to be highly consistent within multiple samples of A. chamissonis) are congruent between the phylogenetic trees based on nrDNA and STL data. Several groups supporting multiple accessions of the same species (of A. To investigate possible congruencies between DNA sequence data and secondary chemistry, we compared nuclear ribosomal DNA (nrDNA) sequence data, sesquiterpene lactone (STL) contents, and cytometric data from 35 accessions of 16 Arnica (Asteraceae) species and two outgroup taxa (Layia hieracioides and Madia sativa), using phylogenetic inference and principal component analysis (PCA). We suggest that historical factors have created this pattern a Mississippi Valley Pleistocene refugium for the American lineage of the species seems plausible. Genetic variation within Vermont was greater within the westward-trending Winooski River watershed than in the Passumpsic River watershed, which drains east into the Connecticut River. Within hemisphere, patterned genetic variation was evident only in the AFLP data and only locally. These two clades have little to no variation even at large geographic scales. Matteuccia struthiopteris segregates globally into minimally divergent (0.3%) Eurasian and American lineages. Here we use DNA sequences and AFLP data to investigate the genetic variation of the fiddlehead fern at two geographic scales to infer the historical biogeography of the species. Much of its current North American and European distribution was covered in ice or uninhabitable tundra during the Pleistocene.
Matteuccia struthiopteris (Onocleaceae) has a present-day distribution across much of the north-temperate and boreal regions of the world. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus‐specific validation efforts. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. Specifically, we use a taxonomy cross‐validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. DNA metabarcoding is an important tool for molecular ecology.