A maximum likelihood approach to the detection of selection from a phylogeny

Summary A large amount of information is contained within the phylogentic relationships between species. In addition to their branching patterns it is also possible to examine other aspects of the biology of the species. The influence that deleterious selection might have is determined here. The likelihood of different phylogenies in the presence of selection is explored to determine the properties of such a likelihood surface. The calculation of likelihoods for a phylogeny in the presence and absence of selection, permits the application of a likelihood ratio test to search for selection. It is shown that even a single selected site can have a strong effect on the likelihood. The method is illustrated with an example fromDrosophila melanogaster and suggests that delerious selection may be acting on transposable elements.     

Prediction of fertilizer phosphate requirement using the Langmuir adsorption maximum

The phosphate adsorption maximum as calculated by the Langmuir equation was used to predict the fertilizer P requirement of wheat (Triticum aestivium, cv. Caldwell) on both virgin and cultivated Decatur clay loam (clayey, kaolinitic, thermic, Rhodic Paleudult) and Hartsells sandy loam soils (fine-loamy, siliceous, thermic, Typic Hapludult). Soils with higher adsorption maximum were found to require more fertilizer P than soils with lower adsorption maximum. For soils 25% saturation of the adsorption maximum gave the optimum dry matter yield. This corresponded to equilibrium P concentration of 0.45 mg L⁻¹ for Decatur cultivated and 0.31 mg L⁻¹ for Decatur and Hartsells virgin soils for optimum dry matter yield. These values are within the range of those reported previously by other investigators working with different soils.     

Feeding and growth of juvenile sea bass: the effect of ration and temperature on growth rate and efficiency

The effect of ration on the growth of pairs of juvenile sea bass Dicentrarchus labrax fed squid mantle was recorded at four temperatures: 6, 10, 14 and 18) C, covering the range typical of Welsh coastal waters. Initial weight of the fish ranged from 2.8 to 15.9 g. A predictive model for the maximum meal size (M_max) at temperatures between 10 and 18) C, accounted for 95% of the variance in lnM_max. Even when offered excess food, bass at 6) C had a low rate of food consumption [0.19% body weight (BW) day^?1] and lost weight (G=?0.04% day^?1). Predictive regression models for specific growth rate (G) accounted for 86% of the variance at reduced rations and 70% at maximum meals. The relationship between G (calculated for total biomass per tank) and ration was a decelerating curve. G at maximum meals increased with temperature, at lower rations G decreased with temperature. For a pair of bass with a combined weight of 15 g, predicted maintenance ration ranged between 0.7 and 2.3% BW day^?1 and increased with temperature. Maximum meal size was more sensitive to temperature than maintenance ration. At 18) C optimum ration was 7.4% BW day^?1. At lower temperatures, the optimum ration was the maximum meal. The maximum gross growth efficiency was 17.4% at 18) C. Mean absorption efficiency was 94.8%. Ration level had no significant effect on absorption efficiency, which was lowest at 6) C. Condition indices (Fulton condition factor, wet and dry liver—somatic indices and body depth index) increased with meal size at all temperatures except 6) C. An increase in temperature between 10 and 18) C generally resulted in a decrease in condition indices at a given ration. When comparisons were made at a given standard length, gut and carcass weight increased with ration. Visceral fat and gut weight decreased with increased temperature.     

Probabilistic reconstruction of ancestral protein sequences

Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales linearly with the number of homologous proteins used to reconstruct the ancestral sequence.     

Molecular evolution of pteridophytes and their relationship to seed plants: Evidence from complete 18S rRNA gene sequences

Complete 18S ribosomal RNA sequence data from representatives of all extant pteridophyte lineages together with RNA sequences from different seed plants were used to infer a molecular phylogeny of vascular plants that included all major land plant lineages. The molecular data indicate that lycopsids are monophyletic and are the earliest diverging group within the vascular land plants, whereasPsilotum nudum is more closely related to the seed plants than to other pteridophyte lineages. The phylogenetic trees based on maximum likelihood, parsimony and distance analyses show substantial agreement with the evolutionary relationships of land plants as interpreted from the fossil record.     

Estimation of the position and effect of a lethal factor locus on a molecular marker linkage map

In the mapping of DNA markers the distortion of segregation of marker genotypes is often observed, which may be caused by a lethal factor acting in filial generations derived from distant crosses. A method is presented for estimating the recombination values between a lethal factor locus and neighboring molecular markers, and the relative viability or fertilization ability of gametes or zygotes affected by the lethal factor in an F₂ population using the maximum likelihood method and the expectation conditional maximization (ECM) algorithm. Three selection models of gamete or zygote were considered, and the most likely one was determined by goodness of fit of the observed frequency of the phenotypes to the expected ones under the models. The method was applied to segregation data of molecular markers of an F₂ population consisting of 144 individuals derived from a cross between an Indica and a Japonica rice variety. The presence of a lethal factor locus (L) located on chromosome III that caused partial gametic selection in both the male and female sides was suggested. The locus L was tightly linked to RFLP marker number 23 of the RFLP linkage map of Saito et al. (1991a), and the fertilization chance of a male or female gamete possessing the lethal factor was, on average, 41.5% of that of the normal gamete.