Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. F_ST outlier analysis revealed that promoter, 5′‐UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within‐population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.     

Improving efficiency of breeding for higher crop yield

Summary Exclusive selection for yield raises, the harvest index of self-pollinated crops with little or no gain in total bipmass. In addition to selection for yield, it is suggested that efficient breeding for higher yield requires simultaneous selection for yield's three major, genetically controlled physiological components. The following are needed: (1) a superior rate of biomass accumulation. (2) a superior rate of actual yield accumulation in order to acquire a high harvest index, and (3) a time to harvest maturity that is neither shorter nor longer than the duration of the growing season. That duration is provided by the environment, which is the fourth major determinant of yield. Simultaneous selection is required because genetically established interconnections among the three major physiological components cause: (a) a correlation between the harvest index and days to maturity that is usually negative; (b) a correlation between the harvest index and total biomass that is often negative, and (c) a correlation between biomass and days to maturity that is usually positive. All three physiological components and the correlations among them can be quantified by yield system analysis (YSA) of yield trials. An additive main effects and multiplicative interaction (AMMI) statistical analysis can separate and quantify the genotype × environment interaction (G × E) effect on yield and on each physiological component that is caused by each genotype and by the different environment of each yield trial. The use of yield trials to select parents which have the highest rates of accumulation of both biomass and yield, in addition to selecting for the G × E that is specifically adapted to the site can accelerate advance toward the highest potential yield at each geographical site. Higher yield for many sites will raise average regional yield. Higher yield for multiple regions and continents will raise average yield on a world-wide basis. Genetic and physiological bases for lack of indirect selection for biomass from exclusive selection for yield are explained.     

Influence of learning on range expansion and adaptation to novel habitats

Learning has been postulated to ‘drive’ evolution, but its influence on adaptive evolution in heterogeneous environments has not been formally examined. We used a spatially explicit individual‐based model to study the effect of learning on the expansion and adaptation of a species to a novel habitat. Fitness was mediated by a behavioural trait (resource preference), which in turn was determined by both the genotype and learning. Our findings indicate that learning substantially increases the range of parameters under which the species expands and adapts to the novel habitat, particularly if the two habitats are separated by a sharp ecotone (rather than a gradient). However, for a broad range of parameters, learning reduces the degree of genetically‐based local adaptation following the expansion and facilitates maintenance of genetic variation within local populations. Thus, in heterogeneous environments learning may facilitate evolutionary range expansions and maintenance of the potential of local populations to respond to subsequent environmental changes.     

Evolution of insecticide resistance in Culex pipiens populations: The Corsican paradox

Culex pipiens mosquitoes from Corsica have been subject to insecticide treatments since 1971, using temephos (an organophosphate). After 17 years, resistance has not developed beyond a 14-fold level. This relatively low resistance is due to the presence of several identified resistance genes, including the insensitive target ( Ace^R ) and overproduced esterases (A1, A4 and B4). The fact that only a low resistance has developed after 17 years of treatment and that this low resistance level is the result of a relatively large number of resistance genes constitute a paradox. To understand this situation and explain why a higher temephos resistance level has not evolved in Corsica as in other parts of the world, it is proposed that the occurrence (through mutation or migration) of efficient resistance genes was a limiting step, and that the only resistance genes available at that time through migration from the surrounding Mediterranean countries had a low cross-resistance to temephos. The local situation of Corsica is discussed in the light of recent data on the world distribution of the known organophosphate resistance genes in this species, and the relative role of mutation and migration in the evolution of insecticide resistance in natural populations.     

Mechanisms of peroxidase oxidation of o-dianisidine, 3,3′,5,5′-tetramethylbenzidine, and o-phenylenediamine in the presence of sodium dodecyl sulfate

Peroxidase oxidation of o-dianisidine, 3,3′,5,5′-tetramethylbenzidine, and o-phenylenediamine in the presence of sodium dodecyl sulfate (SDS), an anionic surfactant, was spectrophotometrically studied. It was found that 0.1–100 mM SDS concentrations stabilize intermediates formed in the peroxidase oxidation of these substrates. The cause of the stabilization is an electrostatic interaction between positively charged intermediates and negatively charged surfactant.     

Population differentiation in Crepis tectorum (Asteraceae): patterns of correlation among characters

This study examines the relationship among traits distinguishing populations of C. tectorum and the extent to which existing trait associations reflect underlying (genetic) tradeoffs. Highly consistent trait associations were found in a comparison of 52 populations representing the western part of the geographical range of the species. In addition to a tight integration of traits reflecting plant stature and inflorescence development, there were consistent links between vegetative and reproductive traits; populations characterized by individuals with large leaves and tall stems with terminal branches usually had larger heads, flowers and fruits (achenes) than those whose individuals had small leaves and a short stem branched from the base. There was a weak negative relationship between the extent of leaf dissection and plant stature; short and compact plants had more deeply lobed leaves than tall plants with terminal branches. Few of these associations were present among families representing a single population of C. tectorum , but there was remarkable similarity between the correlations at the between-population level and those obtained in two segregating F2 progenies of crosses between contrasting populations. Hence, provided that the F2 correlations have a strong genetic basis, it appears that the course of population divergence has been constrained by the underlying correlation structure, although some trait associations may also be a result of selection operating in a correlated fashion on functionally related traits, perhaps leading to linkage disequilibrium of parental traits in the first segregating generation of a cross between ecologically differentiated populations.