Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV.

PREMISE OF THE STUDY: Noncoding chloroplast DNA (NC-cpDNA) sequences are the staple data source of low-level phylogeographic and phylogenetic studies of angiosperms. We followed up on previous papers (tortoise and hare II and III) that sought to identify the most consistently variable regions of NC-cpDNA. We used an exhaustive literature review and newly available whole plastome data to assess applicability of previous conclusions at low taxonomic levels. METHODS: We aligned complete plastomes of 25 species pairs from across angiosperms, comparing the number of genetic differences found in 107 NC-cpDNA regions and matK. We surveyed Web of Science for the plant phylogeographic literature between 2007 and 2013 to assess how NC-cpDNA has been used at the intraspecific level. KEY RESULTS: Several regions are consistently the most variable across angiosperm lineages: ndhF-rpl32, rpl32-trnL((UAG)), ndhC-trnV((UAC)), 5'rps16-trnQ((UUG)), psbE-petL, trnT((GGU))-psbD, petA-psbJ, and rpl16 intron. However, there is no universally best region. The average number of regions applied to low-level studies is ∼2.5, which may be too little to access the full discriminating power of this genome. CONCLUSIONS: Plastome sequences have been used successfully at lower and lower taxonomic levels. Our findings corroborate earlier works, suggesting that there are regions that are most likely to be the most variable. However, while NC-cpDNA sequences are commonly used in plant phylogeographic studies, few of the most variable regions are applied in that context. Furthermore, it appears that in most studies too few NC-cpDNAs are used to access the discriminating power of the cpDNA genome.

Spatial and temporal analysis of pharmaceutical concentrations in the upper Tennessee River basin.

The behavior of pharmaceutical compounds in aquatic ecosystems is not well defined. In order to determine spatial and temporal variations in concentrations of pharmaceuticals in the Tennessee River, water samples were collected from multiple points along the river and at the inflow of major tributaries. Sampling structure was designed to investigate trends between surface and subsurface samples, seasonal trends (winter, spring, summer, and fall), the direct influence of sewage treatment plants (upstream versus downstream), and the effect of downstream distance on pharmaceutical concentrations. All samples were quantified via solid phase extraction followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). This method yielded reproducible quantitation at low parts per trillion (ng L(-1)) levels for all 14 analytes (acetaminophen, atorvastatin, caffeine, carbamazepine, ciprofloxacin, diltiazem, fluoxetine, levofloxacin, lovastatin, norfluoxetine, ranitidine, sertraline, sulfamethoxazole, and trimethoprim). Correlation analyses (depth, distance) and repeated-measures ANOVAs (season, sewage treatment plant proximity) were used to determine statistically significant trends for frequently detected pharmaceuticals (caffeine, carbamazepine, sulfamethoxazole). Caffeine and sulfamethoxazole were found to vary by season in subsurface samples; spring exhibited the highest concentrations. Carbamazepine varied in proximity to sewage treatment plant outfall with subsurface samples yielding greater concentrations downstream than upstream. In addition, individual pharmaceuticals displayed positive correlation between surface and subsurface samples and negative correlation with downstream distance from the headwaters.