Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.     

Factors influencing production of inflorescence-derived somatic seedlings of sweetgum

Somatic embryos derived from staminate inflorescence tissues of three mature sweetgum (Liquidambar styraciflua) trees were tested for germination and conversion frequencies and early growth variables following pregermination cold treatments. Individual mature embryos were selected from repetitively embryogenic cultures maintained on Woody Plant Medium (WPM) with 1 mg l^–1 naphthaleneacetic acid and cultured on basal WPM at 10 8C for 0, 4 or 8 weeks prior to being transferred to WPM germination medium in the light. After 4 weeks, germinated embryos were planted in potting mix in an acclimatization chamber, grown for an additional 8 weeks and evaluated for conversion and growth. Conversion frequency, which ranged up to 80%, was affected by ortet and clonal line, while the number of first-order lateral roots was affected by ortet, clonal line and cold treatment, with 8 weeks of cold promoting the highest number.     

Egg thiamine concentration affects embryo survival in Lake Erie walleye

We quantified thiamine in eggs of Lake Erie walleye to determine if differences exist between spawning stocks within the Maumee and Sandusky rivers, both of which drain into the Western Basin. In spring 2004, eggs of walleye were collected in the Maumee River at three occasions (early, peak and late of the spawning run) and in the Sandusky River during the spawning run. After collection, eggs were fertilized with a known amount of milt, incubated and embryo survival was determined at the pigmented eyed stage. Thiamine and its derivatives were analyzed using high performance liquid chromatography. Thiamine pyrophosphate (TPP) was the most abundant form of vitamin B₁ present in eggs (60–95% of the total vitamin B₁ concentration). Total thiamine concentrations in walleye eggs from the Maumee and Sandusky rivers at the peak of the spawning run averaged 6.1 ± 1.6 nmol g⁻¹ and 5.0 ± 2.9 nmol g⁻¹, respectively. Our results also indicated that Maumee River stock survival to the eyed stage embryo declined as the spawning season progressed (72%, 59% and 37% in the early, middle and late of spawning run, respectively) as well as the total thiamine and TPP concentrations. At the peak of the spawning run, survival to the eyed stage embryo did not differ significantly between stocks 59% versus 65% in the Maumee and Sandusky rivers, respectively, and thiamine concentrations were not significantly different between sites.     

Actin assembly activity of cytochalasins and cytochalasin analogs assayed using fluorescence photobleaching recovery

The effects on actin self-assembly of 9 common cytochalasins and 9 synthetic analogs have been assayed using fluorescence photobleaching recovery (FPR). The specific assembly activities of cytochalasins determined by this assay are (i) reduction of the fraction of actin molecules incorporated into filaments; (ii) increase of the steady-state diffusion coefficients of filaments, from which filaments shortening may be inferred; and (iii) acceleration of the initial rate of assembly. Of the compounds studied, only cytochalasin D shows strong activity of all three types. The range of activities shown by other compounds indicates clearly that these three activity types are distinct and independent. Inspection of the molecular structures of these 18 compounds for correlation of structure and activity reveals that the three different activities depend on distinct structural features. The Mg2+ dependence of filament-shortening activity by certain cytochalasins may be explained by the Mg2+ chelating ability of two suitably positioned oxygen atoms on the convex face of the bicyclic isoindolone system. Inhibition of filament elongation may involve very specific, high-affinity cytochalasin interactions at a binding site on terminal actin molecules, while accelerating activity may occur by weaker, less specific binding interactions of cytochalasins with monomeric actin.     

Assessing support for Blaberoidea phylogeny suggests optimal locus quality

Phylogenomics seeks to use next‐generation data to robustly infer an organism's evolutionary history. Yet, the practical caveats of phylogenomics motivate investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in Blaberoidea. We examine locus substitution rate, saturation, evolutionary divergence, rate heterogeneity, stabilizing selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species. Loci with high substitution rate, low saturation, low sequence distance, low rate heterogeneity, and strong stabilizing selection derive more support for phylogenetic relationships. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction, improved statistical support, and potential 4‐6x improvements to computation time. Supported by phylogenetic and morphological evidence, we erect three newly named clades (Anallactinae Evangelista & Wipfler subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux and Hemithyrsocerini Evangelista tribe nov.) and propose other taxonomic modifications. The diagnosis of Pseudophyllodromiidae Grandcolas, 1996 is modified to accommodate Anallactinae and Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel morphological characters.     

Effect of sterol incorporation on head group separation in liposomes

Electrophoretic mobilities of multilamellar liposomes of varying composition have been measured to determine the effect of incorporated sterols on surface charge density. Liposomes made from mixtures of zwitterionic egg phosphatidylcholine (PC) and anionic egg phosphatidylglycerol (PG) in varying proportions were shown to have electrophoretic mobilities consistent with the anticipated surface charge density. Incorporation of cholesterol up to 50 mole per cent in the bilayer produced no detectable change in surface charge density. Similar results were obtained for lanosterol and epicoprostanol. These results are interpreted to mean that incorporation of the sterols into the bilayers produced no detectable change (less than 3%) in the spacing of charged phospholipids. It is inferred that sterols are incorporated among the fatty acyl chains of these phospholipid bilayers with little or no displacement of the head groups at the surface.