Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.     

Effect of dietary copper sulfate, Aureo SP250, or clinoptilolite on ureolytic bacteria found in the pig large intestine

The predominant ureolytic bacteria in the pig large intestine were determined while growing pigs were fed a basal diet or basal diet plus copper sulfate, Aureo SP250, or clinoptilolite. Fecal samples were collected from four pigs fed each diet at 3, 9, and 14 weeks and analyzed for total colony counts and percent ureolytic bacteria. Fecal urease activity, ammonia nitrogen, and identity of the ureolytic bacteria were determined at 14 weeks. Copper sulfate and Aureo SP250 reduced the number of ureolytic organisms, with a marked decrease occurring in the Streptococcus spp., which made up 74% of the ureolytic isolates from the pigs on the basal diet. Other ureolytic species detected at lower concentrations were Staphylococcus spp., Selenomonas ruminantium, Bacteroides multiacidus, and Eubacterium limosum. Copper sulfate also reduced fecal urease activity (P less than 0.10). Fecal ammonia concentrations were not different between pigs fed the various diets. These data suggest that the streptococci are the most numerous ureolytic species in the pig intestinal tract and are significantly reduced by copper sulfate and Aureo SP250; however, only copper sulfate reduced intestinal urease activity.     

Oxygen consumption by portal vein-drained organs and by whole animal in conscious growing swine

A method was developed to measure simultaneously the O2 consumption (VO) by the whole animal and by the hepatic portal vein-drained organs (PVDO), including the gastrointestinal tract, spleen, and pancreas in conscious 3.5- to 4-month-old swine. The method was used to determine (i) the effect of feeding on hepatic portal vein blood flow rate (Qpv) and VO by PVDO and by the whole animal, and (ii) the significance of PVDO on the oxidative demand in the pig. Chronic cannulas were placed in the hepatic portal vein, carotid artery, and ileal vein. The Qpv was determined by an indicator dilution technique employing continuous constant infusion of 1% p-aminohippuric acid into the ileal vein. The VO2 by PVDO was estimated by multiplying Qpv by arterial-portal vein O2 difference measured with an arterial-venous O2 difference analyzer connected to the carotid artery and portal vein cannulas. Whole animal VO2 was measured with an open circuit indirect calorimeter. In seven pigs (3.5- to 4-month-old, 37.4 +/- 0.8 kg) trained to be fed once daily, feeding (1.2 kg of feed mixed with 1.2 liter of H2O) caused postprandial (6 hr) Qpv to increase more than 34 +/- 15% above the preprandial value of 34.5 +/- 4.2 ml.min-1.kg-1 body wt. The postprandial VO2 by PVDO was elevated more than 46 +/- 12% above the value of 1.52 +/- 0.20 ml.min-1.kg-1 body wt observed during the preprandial period. Whole animal VO2 increased 45 +/- 9 and 33 +/- 7% above the preprandial value of 6.23 +/- 0.57 ml.min-1.kg-1 body wt for the first 6 hr and the 7 to 12 hr after feeding, respectively. Although PVDO represent only 5% of body weight, they used 25% of whole body VO2. The study clearly illustrates the significance of PVDO on the whole animal oxidative demand in conscious growing swine.     

R-body-producing bacteria.

Until 10 years ago, R bodies were known only as diagnostic features by which endosymbionts of paramecia were identified as kappa particles. They were thought to be limited to the cytoplasm of two species in the Paramecium aurelia species complex. Now, R bodies have been found in free-living bacteria and other Paramecium species. The organisms now known to form R bodies include the cytoplasmic kappa endosymbionts of P. biaurelia and P. tetraurelia, the macronuclear kappa endosymbionts of P. caudatum, Pseudomonas avenae (a free-living plant pathogen), Pseudomonas taeniospiralis (a hydrogen-oxidizing soil microorganism), Rhodospirillum centenum (a photosynthetic bacterium), and a soil bacterium, EPS-5028, which is probably a pseudomonad. R bodies themselves fall into five distinct groups, distinguished by size, the morphology of the R-body ribbons, and the unrolling behavior of wound R bodies. In recent years, the inherent difficulties in studying the organization and assembly of R bodies by the obligate endosymbiont kappa, have been alleviated by cloning and expressing genetic determinants for these R bodies (type 51) in Escherichia coli. Type 51 R-body synthesis requires three low-molecular-mass polypeptides. One of these is modified posttranslationally, giving rise to 12 polypeptide species, which are the major structural subunits of the R body. R bodies are encoded in kappa species by extrachromosomal elements. Type 51 R bodies, produced in Caedibacter taeniospiralis, are encoded by a plasmid, whereas bacteriophage genomes probably control R-body synthesis in other kappa species. However, there is no evidence that either bacteriophages or plasmids are present in P. avenae or P. taeniospiralis. No sequence homology was detected between type 51 R-body-encoding DNA and DNA from any R-body-producing species, except C. varicaedens 1038. The evolutionary relatedness of different types of R bodies remains unknown.     

Body weight deficit in the absence of reduction in cerebrum weight and nucleic acid content in progeny of swine restricted in protein intake during pregnancy

Fifty-six castrated male progeny of crossbred (Chester White x Landrace x Large White x Yorkshire) dams fed an adequate diet (control, C), a control diet fed at one-third of C (restricted, R), or diets severely deficient in protein (PF) or restricted in nonprotein calories (RCal) were killed at age 25 weeks. Dams were fed their respective diets in the following regimens: C, 1.8 kg (6000 kcal daily) throughout pregnancy; R, 0.6 kg of C diet daily for 70 days, then 1.8 kg of C daily to parturition at about 114 days; PF, 1.8 kg of a "protein-free" diet (less than 0.2% protein) throughout pregnancy; RCal, 0.6 kg daily (2000 kcal) of a diet containing three times the concentration of protein, minerals, and vitamins provided by the C diet for 70 days, then 1.8 kg of C daily to parturition. All dams were fed an adequate diet ad libitum through a 28-day lactation. Castrated male progeny were assigned to one of two replicates based on birth date and fed a corn-soybean meal diet ad libitum from weaning to age 25 weeks, supplemented from age 10 to 12 weeks with 0, 110, or 220 mg/kg of thyroprotein (iodinated casein). Cerebrum weight was unaffected by maternal diet, despite a significant (P less than 0.001) reduction in body weight of progeny of PF dams compared with other groups, resulting in a higher relative cerebrum weight in progeny of PF dams than in progeny of C, R, and RCal dams. Absolute and relative weights of RNA, DNA, and total protein in cerebrum were unaffected by maternal diet. Thyroprotein supplementation to the diet of the progeny had no effect on cerebrum weight or its protein or nucleic acid content. It is concluded that maternal protein deprivation but not restriction of feed or nonprotein calorie intake to one-third of recommended allowance during gestation results in stunting of body weight in young adult progeny but does not affect cerebrum weight, cerebrum cell number (DNA), or protein synthetic activity (RNA), or RNA-to-protein ratio.     

Adventitious shoot formation in cultures of 30-year-old Larix decidua,L. leptolepis,L. eurolepis,and L. laricina trees

Primordial shoot explants excised from buds of one Larix decidua tree, about 30 years old, produced more adventitious buds, elongating into shoots, when grown on half strength Litvay medium than when grown on other basal media. Thidiazuron and N₆-benzyladenine (BA) were equally effective in adventitious bud induction. In a comparative study of 30-year-old L. decidua, L. leptolepis, L. eurolepis, and L. laricina trees, explants from L. eurolepis and L. decidua produced a high number of cultures with adventitious buds that elongated into shoots; those from L. leptolepis were less productive, and those from L. laricina failed to form adventitious buds. The highest response was obtained with material collected in August and September, and in March and April; the lowest response occurred in explants from the October collection.     

Locomotion and bone strength of the white rhinoceros, Ceratotherium simum

Measurements have been made, of lengths and of geometric properties of cross-sections, of the long bones of the legs of a young white rhinoceros of about 750 kg body mass. These are considered in conjunction with data from film of white rhinoceros trotting and galloping. The stresses developed in the bones in running are rather low, in comparison with other large mammals, suggesting that rhinoceros skeletons may be built to unusually high factors of safety. The long, relatively straight legs of elephants (whose bones experience higher stresses) are contrasted with the shorter, less straight legs of the other graviportal mammals.     

Characterization of Caedibacter endonucleobionts from the macronucleus of Paramecium caudatum and the identification of a mutant with blocked R-body synthesis

Cytology, DNA and host-symbiont relationships of x-like endosymbionts from Paramecium caudatum are described. The symbionts (Caedibacter caryophila, sp. nov.) live in the macronuclei of their hosts. They confer the killer trait upon their hosts and appear well adapted to their endonucleobiotic way of life. R bodies (proteinaceous ribbons associated with killing) are produced, but differ significantly from any of the four R-body classes previously described. C. caryophila and their R bodies were isolated. DNA was extracted from purified symbionts and used to demonstrate that one P. caudatum line harbors a natural mutant which is deficient in R-body production. Melting studies indicate a GC content of 34.6%. No sequence homology between the C. caryophila DNA and the coding sequence for type 51 R-body production was observed. C. caryophila is parasitic, causing the death of its hosts in starving cultures.     

Effect of salinity on mycorrhizal onion and tomato in soil with and without additional phosphate

Summary Vesicular-arbuscular mycorrhizal fungi (VAM) are known to increase plant growth in saline soils. Previous studies, however, have not distinguished whether this growth response is due to enhanced P uptake or a direct mechanism of increased plant salt tolerance by VAM. In a glasshouse experiment onions (Allium cepa L.) were grown in sterilized, low-P sandy loam soil amended with 0, 0.8, 1.6 mmol P kg^–1 soil with and without mycorrhizal inoculum. Pots were irrigated with saline waters having conductivities of 1.0, 2.8, 4.3, and 5.9 dS m^–1. Onion colonized withGlomus deserticola (Trappe, Bloss, and Menge) increased growth from 394% to 100% over non-inoculated control plants when soil P was low ( 0.2 mmol kg^–1 NaHCO₃-extractable P) at soil saturation extract salinities from 1.1 dS m^–1 to 8.8 dS m^–1. When 0.8 and 1.6 mM P was added no dry weight differences due to VAM were observed, however, K and P concentrations were higher in VAM plants in saline treatments.Glomus fasciculatum (Gerdeman and Trappe) andGlomus mosseae (Nicol. and Gerd.) isolates increased growth of VAM tomato 44% to 193% in non-sterilized, saline soil (10 dS m^–1 saturation extract) despite having little effect on growth in less saline conditions when soil P was low. Higher tomato water potentials, along with improved K nutrition by VAM in onion, indicate mechanisms other than increased P nutrition may be important for VAM plants growing under saline stress. These effects appear to be secondary to the effects of VAM on P uptake.     

Enumeration and activity of cellulolytic bacteria from gestating swine fed various levels of dietary fiber

Cellulolytic bacteria were enumerated and cellulase activity was determined over a 98-day period from fecal samples of gestating swine fed various levels and sources of fiber. The diets, each fed to five pigs, were a corn-soybean control, 20% corn cobs, and 40 and 96% alfalfa meal. Fecal samples were collected from all pigs on days 0, 5, 14, 21, 35, 49, 70, and 98. Overall, the most probable number of cellulolytic bacteria from pigs fed the control, 20% corn cobs, and 40 and 96% alfalfa meal was 23.3 X 10(8), 15.2 X 10(8), 45.1 X 10(8), and 52.5 X 10(8) per g (dry weight) of fecal sample, respectively. Enumeration of cellulolytic bacteria by counting zones of clearing in roll tubes, as compared with the most probable number procedure, accounted for only 1.1 and 17.0% of the cellulolytic bacteria, respectively, from pigs fed the control or 96% alfalfa meal diet. Cellulolytic bacteria (most probable number) on days 70 and 98 accounted for 4.1 and 10.0% of the viable count for the pigs fed the control and 96% alfalfa meal diets, respectively. The viable count was not different between pigs fed the control and 96% alfalfa meal diets. The overall mean cellulolytic activity (milligrams of glucose released from carboxymethyl cellulose per gram [dry weight] fecal sample per 30 min was 17.0, 19.9, 23.8, and 20.6, respectively, for the control, 20% corn cobs, and 40 and 96% alfalfa meal diets. The results indicate that the cellulolytic flora can be increased by prolonged feeding of high-fiber diets and may represent 10% of the culturable flora.