Population genomics from pool sequencing

Next generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator , nucleotide pairwise diversity Π, Tajima's D, Fu and Li's D and F, Fay and Wu's H, McDonald‐Kreitman and HKA tests and , corrected for sequencing errors and ascertainment bias. In a simulation study, we show that pool and individual θ estimates are highly correlated and discuss how the performance of the statistics vary with read depth and sample size in different evolutionary scenarios. As an application, we reanalyse sequences from Drosophila mauritiana and from an evolution experiment in Drosophila melanogaster. These methods are useful for population genetic projects with limited budget, study of communities of individuals that are hard to isolate, or autopolyploid species.     

Modified Whole Effluent Toxicity Test to Assess and Decouple Wastewater Effects from Environmental Gradients

Environmental gradients and wastewater discharges produce aggregated effects on marine populations, obscuring the detection of human impact. Classical assessment methods do not include environmental effects in toxicity tests designs, which could lead to incorrect conclusions. We proposed a modified Whole Effluent Toxicity test (mWET) that includes environmental gradients in addition to effluent dilutions, together with the application of Generalized Linear Mixed Models (GLMM) to assess and decouple those effects. We tested this approach, analyzing the lethal effects of wastewater on a marine sandy beach bivalve affected by an artificial canal freshwater discharge used for rice crops irrigation. To this end, we compared bivalve mortality between canal water dilutions (CWd) and salinity controls (SC: without canal water). CWd were prepared by diluting the water effluent (sampled during the pesticide application period) with artificial marine water. The salinity gradient was included in the design by achieving the same final salinities in both CWd and SC, allowing us to account for the effects of salinity by including this variable as a random factor in the GLMM. Our approach detected significantly higher mortalities in CWd, indicating potential toxic effects of the effluent discharge. mWET represents an improvement over the internationally standardized WET tests, since it considers environmental variability and uses appropriate statistical analyses.     

Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency

Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.     

ABA and GA3 increase carbon allocation in different organs of grapevine plants by inducing accumulation of non‐structural carbohydrates in leaves,enhancement of phloem area and expression of sugar transporters

Grape quality for winemaking depends on sugar accumulation and metabolism in berries. Abscisic acid (ABA) and gibberellins (GAs) have been reported to control sugar allocation in economically important crops, although the mechanisms involved are still unknown. The present study tested if ABA and gibberellin A₃ (GA₃) enhance carbon allocation in fruits of grapevines by modifying phloem loading, phloem area and expression of sugar transporters in leaves and berries. Pot‐grown Vitis vinifera cv. Malbec plants were sprayed with ABA and GA₃ solutions. The amount of soluble sugars in leaves and berries related to photosynthesis were examined at three points of berry growth: pre‐veraison, full veraison and post‐veraison. Starch levels and amylase activity in leaves, gene expression of sugar transporters in leaves and berries and phloem anatomy were examined at full veraison. Accumulation of glucose and fructose in berries was hastened in ABA‐treated plants at the stage of full veraison, which was correlated with enhancement of Vitis vinifera HEXOSE TRANSPORTER 2 (VvHT2) and Vitis vinifera HEXOSE TRANSPORTER 6 (VvHT6) gene expression, increases of phloem area and sucrose content in leaves. On the other hand, GA₃ increased the quantity of photoassimilates delivered to the stem thus increasing xylem growth. In conclusion, stimulation of sugar transport by ABA and GA₃ to berries and stems, respectively, was due to build‐up of non‐structural carbohydrates in leaves, modifications in phloem tissue and modulation in gene expression of sugar transporters.     

Comparative life cycle assessment of first- and second-generation ethanol from sugarcane in Brazil

The International Journal of Life Cycle Assessment - The use of bagasse and trash from sugarcane fields in ethanol production is supposed to increase the ethanol yield per hectare, to reduce the...     

No correlation between inbreeding depression and delayed selfing in the freshwater snail Physa acuta

Inbreeding depression, one of the main factors driving mating system evolution, can itself evolve as a function of the mating system (the genetic purging hypothesis). Classical models of coevolution between mating system and inbreeding depression predict negative associations between inbreeding depression and selfing rate, but more recent approaches suggest that negative correlations should usually be too weak or transient to be detected within populations. Empirical results remain unclear and restricted to plants. Here, we evaluate, for the first time, the within-population genetic correlation between inbreeding depression and a trait that controls the amount of self-fertilization (the waiting time) in a self-fertile hermaphroditic animal, the freshwater snail Physa acuta. Using a large quantitative-genetic design (36 grand-families and 348 families), we observe abundant within-population family-level genetic variation for both inbreeding depression (estimated for survival, fecundity, and size) and the degree of behavioral selfing avoidance. However, we detected no correlation between waiting time and inbreeding depression across families. In agreement with recent models, this result shows that mutational variance rather than differential purging accounts for most of the genetic variance in inbreeding depression within a population.     

A novel in vitro propagation system for West Indian elm [Guazuma ulmifolia Lam. (Malvaceae)]: a valuable medicinal woody species

In Vitro Cellular & Developmental Biology - Plant - The aim of this study was to establish a system of in vitro germination and propagation of Guazuma ulmifolia Lam. microcuttings (Malvaceae)....     

Effects of follicular status at treatment on follicular development and ovulation in response to FSH in Spanish merino ewes

Cyclic Spanish Merino ewes were treated on Day 13 of the estrous cycle with 12 mg, i.m., FSH-P in saline (n = 9) or propylene glycol (n = 24), currently with 100 micrograms, i.m., Cloprostenol (Day 0). From Day-6 to Day 0, the ewes were observed daily by transrectal ultrasonography, after Day 0, ultrasonography was performed every 12 h for 72 h. Sizes and locations of > or = 2 mm follicles were recorded at each observation. The ovulation rate was determined by laparoscopy on Day 7 after estrus. The number of ovulations ranged from 0 to 6 in ewes treated with FSH-P in saline and from 0 to 16 in ewes receiving FSH-P in propylene glycol (P < 0.05). In the latter group, the response was bimodally distributed; about half of the females had 1 ovulation, whereas the remainder had > 4 with a mean of 7 ovulations. The ovulation rate was associated with 2 characteristics of the largest follicle present at treatment (Day 0). First, if the largest follicle on Day 0 had not changed in diameter from Day-1 to Day 0, then 7 of 9 ewes had > 3 ovulations; if the largest follicle had either increased or decreased, only 8 of 24 ewes had > 3 ovulations (P < 0.05). Second, there was a linear trend (P < 0.07) for ovulation rate to decrease as the persistence of the largest follicle at treatment increased; no ewe in which the largest follicle on Day 0 remained present for more than 36 h ovulated more than 6 follicles. As with the ovulation rate, the numbers of large follicles on Days 1.5, 2 and 2.5 varied with the interaction of change in diameter of the largest follicle on Day 0 from Day-1 to Day 0 and with vehicle. In summary, the superovulatory response was affected by the change in diameter from Day-1 to Day 0 of the largest follicle on Day 0 and the period required for that follicle to regress after treatment with FSH-P and cloprostenol.