Genetic evaluation with uncertain parentage: a comparison of methods

Summary The most common method for genetic evaluation when parents are unknown is best linear unbiased prediction with genetic groups (BLUP-G). With this method unknown parents are assumed to be unrelated to any other animals in the population. This assumption is unrealistic in most situations. If a finite number of potential parents can be identified and the probabilities of being the true parent can be assigned to these, genetic evaluation can be obtained given the uncertainty of parentage without introducing genetic groups into the model. The correct numerator relationship matrix with uncertain parentage () is derived. Rules are given to efficiently compute and ^-1. Computer simulation was used to compare BLUP-G with BLUP using . The simulated population consisted of ten sires and 200 dams per breeding season. The dams were always known; the sires were unknown for 10% or 30% of the males and 30% of the females. The number of potential sires was three (BLUP-₁ or ten (BLUP-₂), including the true sire in both cases. Equal probabilities were assigned to each potential sire. The increase in response with BLUP-₁ and BLUP-₂ relative to BLUP-G ranged from 4% to 8% in the fifth breeding season. Selection with BLUP-₁ or BLUP-₂ resulted in higher inbreeding, 17% and 12%, respectively, than with BLUP-G. Estimates of response to selection were unbiased with BLUP-₁ and BLUP-₂, but not unbiased with BLUP-G. Mean square error of estimated genetic means and mean prediction error variance were higher with BLUP-G than with blup-₁ or BLUP-₂.     

Population census of the chimpanzees in the Kalinzu Forest,Uganda: Comparison between methods with nest counts

The population of chimpanzees in the Kalinzu Forest, Uganda was censused with nest counts using the line-transect method. Four methods were examined to estimate density. The estimated densities, ranging from 2.0 to 4.7 chimpanzees per km², all indicated a high population density, in comparison with other chimpanzee habitats. Moreover, the density in the logged area of the Kalinzu Forest was higher than that in the unlogged area. Several factors are thought to contribute to the high density in the Kalinzu Forest. Notable are the mosaic forest structure dominated by mature forest with patches of logged areas, selective logging of non-food tree species of chimpanzees, and low hunting pressure. These results suggest that selective logging may be a practical means of primate conservation in places where timbers are exploited.     

Above-ground biomass changes over an 11-year period in an Amazon monodominant forest and two other lowland forests

Tropical rain forest dominated by Peltogyne gracilipes (Fabaceae) occurs on Maracá Island, Roraima, Brazil, on a range of soil types. Three forest types were stratified for sampling, according to the occurrence of Peltogyne trees: (1) Peltogyne-rich forest (PRF), (2) Peltogyne-poor forest (PPF), and (3) forest without Peltogyne (FWP). Biomass increment and change in total stand biomass were calculated from mortality, recruitment, and growth data for trees in the three forest types. Data were derived from permanent plots established in 1991, where all trees (≥10 cm diameter at breast height), including palms and vines (lianas), were tagged and measured in three plots, each of 0.25 ha, in each of the three forest types. Field surveys were carried out in October 1991 and March 2003. Over a period of 11 years, the above-ground biomass in all forest types declined slightly (<5%), associated with the death of large trees, especially in the monodominant forests (PRF and PPF). Within the study period, the forest on Maracá experienced two heavy droughts, related to El Niño events (1997–1998 and 2002–2003) and most mortality and loss of biomass probably occurred during these events. Therefore, as the Maracá forests appear not be increasing in above-ground biomass overall, they may not be acting as a sink for atmospheric CO₂. The trees of the five most abundant species (Ecclinusa, Lecythis, Licania, Peltogyne, and Pradosia) accounted for about 55% of the total biomass in both FWP and PPF and for 74% in PRF. Peltogyne gracilipes had a stable, regenerating population in PRF, and is clearly a persistent dominant in a monodominant forest.     

Cellulase activities in biomass conversion: measurement methods and comparison

Cellulose, the major constituent of all plant materials and the most abundant organic molecule on the Earth, is a linear biopolymer of glucose molecules, connected by β-1,4-glycosidic bonds. Enzymatic hydrolysis of cellulose requires mixtures of hydrolytic enzymes including endoglucanases, exoglucanases (cellobiohydrolases), and β-glucosidases acting in a synergistic manner. In biopolymer hydrolysis studies, enzyme assay is an indispensable part. The most commonly used assays for the individual enzymes as well as total cellulase activity measurements, including their advantages and limitations, are summarized in this review article. In addition, some novel approaches recently used for enzyme assays are summarized.     

A comparison of different methods used for the quantitative evaluation of biomass of freshwater phytoplankton

Although in a strict sense the term phytoplankton biomass only refers to living algal material, in aquatic ecology the term has been associated with a variety of biological and biochemical procedures used to quantify the particulate matter suspended in natural waters. Relative merits of different biomass characteristics have been studied in three Dutch freshwater lakes with great differences in absolute biomass. Parallel determinations have been made of seston dry weight and supplementary elementary and caloric analyses of seston, of chlorophyll-a concentration and supplementary paper chromatographic analyses of pigment extracts, of particle concentration and particle size distribution as studied with an electronic particle counter, and of phytoplankton cell volume as calculated from the results of microscopic enumeration and sizing of algae. In this way an attempt was made to create a detailed picture of the nature of the seston of the three freshwater lakes.Different analytical techniques give strikingly different information, the accuracy of any method is largely dependent on the circumstances present, and different biomass characteristics therefore are only of value in limited spheres. It is suggested to distinguish between total seston characteristics (e.g. seston dry weight, particulate organic carbon, total particle volume) and strictly algological biomass characteristics (e.g. chlorophyll-a concentration, phytoplankton cell volume). The pattern of growth of phytoplankton populations shown by e.g. chlorophyll-a concentration may differ markedly from that indicated by e.g. total particle volume or seston dry weight. Also, to more or less extent the wax and wane of phytoplankton populations may go undetected among the total seston. Apparently, there is no one method of estimating biomass and no conversion factor that may serve for general purposes. In general, unambiguous information on the nature of the seston of natural waters may only be obtained by estimating total seston characteristics and algological biomass characteristics simultaneously. Depending on the objective of the investigation supplementary component analyses should be carried out to guarantee the correct interpretation of the results.     

Fractionation of sediment phosphate with chelating compounds: a simplification, and comparison with other methods

The NTA/EDTA fractionation of sediment-bound, inorganic phosphate was improved and made more effective. The iron-bound phosphate is now extracted with Ca-EDTA plus dithionite and followed by an extraction of calcium-bound phosphate by Nat-EDTA at pH = 4.5. A comparison is made with two other sequential extraction procedures: the SEDEX and the Hieltjes & Lijklema extractions. The EDTA extractions have an advantage over the other two methods.     

Estimating primate densities using home range and line transect methods: A comparative test with the black colobus monkeyColobus satanas

The line transect method is one of the main methods used to estimate primate densities. Several protocols have been proposed to analyze the data recorded under this method but none of them have been widely accepted since there is a considerable controversy about their respective accuracy. In this study, densities of the black colobus monkeyColobus satanas calculated using eight different protocols were compared with the actual density given by the home range method. Rates of polyspecific associations were also compared. The two most accurate estimates of group density (under- or overestimation <10%) were yielded by the protocol that used the maximum transect-to-animal distance and by that of using a fixed distance of 100 m. These protocols, however, underestimated individual density because counts performed from transects underestimated by 23% the average group size. The six other protocols overestimated group density by 20–195%. Factors that could explain these overestimation were discussed. Because histogram of sighting frequency showed several classes of distances with no records and because groups have been detected as far as 160 m, we suggested that the uneven topography of the study site increased the variability of the sighting distances. Combined with a relatively low number of sightings (n=23), this did not allow to identify a sharp detection distance. Rates of polyspecific association found with the two methods were similar. We recommend to investigate the influence of the topography for bias in density estimates when using the line transect method.     

The changes in China's forests: an analysis using the Forest Identity

Changes in forest carbon stocks are a determinant of the regional carbon budget. In the past several decades, China has experienced a pronounced increase in forest area and density. However, few comprehensive analyses have been conducted. In this study, we employed the Forest Identity concept to evaluate the changing status of China''s forests over the past three decades, using national forest inventory data of five periods (1977–1981, 1984–1988, 1989–1993, 1994–1998, and 1999–2003). The results showed that forest area and growing stock density increased by 0.51% and 0.44% annually over the past three decades, while the conversion ratio of forest biomass to growing stock declined by 0.10% annually. These developments resulted in a net annual increase of 0.85% in forest carbon sequestration, which is equivalent to a net biomass carbon uptake of 43.8 Tg per year (1 Tg = 10¹² g). This increase can be attributed to the national reforestation/afforestation programs, environmentally enhanced forest growth and economic development as indicated by the average gross domestic product.     

Neurogenesis in adult primate neocortex: an evaluation of the evidence

Reports of continuous genesis and turnover of neurons in the adult primate association neocortex--the site of the highest cognitive functions--have generated great excitement. Here, I review the available evidence, and question the scientific basis of this claim.     

Activity and Ranging Patterns of Guerezas in the Kakamega Forest: Intergroup Variation and Implications for Intragroup Feeding Competition

From March 1997 to February 1998, I investigated the activity patterns of 2 groups and the ranging patterns of 5 groups of eastern black-and-white colobus (Colobus guereza), aka guerezas, in the Kakamega Forest, Kenya. Guerezas at Kakamega spent more of their time resting than any other population of colobine monkeys studied to date. In addition, I recorded not one instance of intragroup aggression in 16,710 activity scan samples, providing preliminary evidence that intragroup contest competition may be rare or absent among guerezas at Kakamega. Mean daily path lengths ranged from 450 to 734 m, and home range area ranged from 12 to 20 ha, though home range area may have been underestimated for several of the study groups. Home range overlap was extensive with 49–83% of each group's range overlapped by the ranges of other groups. Despite the high level of home range overlap, the frequently entered areas (quadrats entered on 30% of a group's total study days) of any one group were not frequently entered by any other study group. Mean daily path length is not significantly correlated with levels of availability or consumption of any plant part item. Mean daily path length is also not significantly correlated with group size, though the largest group did have the longest mean daily path length. This finding suggests that intragroup scramble competition may have been rare or absent among guerezas at Kakamega except perhaps in the largest group, which was unusually large.     

MaxBench: evaluation of sequence and structure comparison methods

SUMMARY: MaxBench is a web-based system available for evaluating the results of sequence and structure comparison methods, based on the SCOP protein domain classification. The system makes it easy for developers to both compare the overall performance of their methods to standard algorithms and investigate the results of individual comparisons. AVAILABILITY: http://www.sanger.ac.uk/Users/lp1/MaxBench/     

Use of Victoria blue in the detection of intrahepatocyte HBs Ag: comparison with other methods

The authors tested Victoria blue staining in intrahepatocytic HBs Ag detection and compared the results with those obtained by the following methods: direct immunofluorescence, orcein and peroxidase-antiperoxidase (PAP). Although PAP appears to be the best technique for diagnostic research, Victoria blue is a sound method for routine diagnosis in hepatology.     

Estimation of soil algal biomass in salinized irrigation land: a comparison of culture dilution and chlorophyll a extraction methods

Two representative methods for quantitative estimation of soil algae, the culture dilution method and chlorophyll a extraction, were compared using soil samples collected from irrigation land in the flood plain of the River Ili, Kazakhstan, where the distribution of soil algae had been studied in the previous year. The estimate by the culture dilution method was almost the same as in the previous year, except for one site, which was enclosed by shrubs of sakusaul, Haloxylon aphyllum (Minkw.) Iljin. The important role of wind in transport of airborne algal cells was pointed out. There was a significant correlation (p<0.001) between the logarithm of the number of colonies by the culture dilution method andthe logarithm of the concentration of chlorophyll a, when data from all samples were analyzed. However, no significant correlation was observed with the data of cropland sites alone. Furthermore, the seasonal variations of both values at each site did not necessarily agree with each other. One reason for the inconsistency may have been the over estimation of chlorophyll a caused by inclusion of litter from vascular plants. Other reasons may relate to differences between the methodologies. The density of soil algae estimated by culture dilution reflects the algal biomass in a certain previous period of time. Therefore, it is suggested that the method is suitable for spatial, but not for seasonal studies. This revised version was published online in August 2006 with corrections to the Cover Date.     

A single-bottle blood culture system: evaluation and comparison with two other systems.

A commercially available single-bottle blood culture system was evaluated at Ben Taub General Hospital, a Harris County District Hospital. Blood cultures from 1010 patients were examined with the Lederle Diagnostics one-bottle blood culture medium-SPS, Columbia broth (E-Vac, Pfizer), and an in-house-prepared brain heart infusion broth with p-aminobenzoic acid (PABA) and 0.1% agar. Of the 1010 patients examined, blood cultures from 211 (20.8%) were positive, yielding a total of 23 different species of microorganisms. Comparison of the results during clinical evaluation, as well as those from simulated blood cultures, showed that the Lederle Diagnostics blood culture bottle was as effective as the in-house-prepared brain heart infusion and commercially available Columbia broths for isolation of aerobes as well as anaerobes. The techniques used in the evaluation and the advantages of a single-bottle culture system are discussed.     

A comparison of three methods of measuring phytoplankton biomass on a daily and seasonal basis

Three methods of measuring phytoplankton biomass (microscopic counting, electronic particle counting and determination of chlorophyll a concentration) were compared on both a daily (4 days) and a seasonal basis, in Charnwood Water, a small English freshwater lake. Correlations among measures were generally poor within days. However, good correlations were achieved among all methods on a seasonal basis. Seasonal correlations, in particular those between total particle numbers from particle counting and algal numbers from microscope, were affected by the degree of stability of the water column, with different relationships being found for mixed periods compared to stratified periods. These differences were related to an increased amount of particulate matter affecting the total particle numbers estimate during mixed periods. Other workers have found better relationships among these phytoplankton biomass methods within short periods, but there appears to be considerable variability among lakes. Therefore, it is recommended that the most appropriate method be evaluated on a individual lake basis, depending on the aims of the study.     

Phytoplankton of an eutrophic tropical reservoir: comparison of biomass estimated from counts with chlorophyll-a biomass from HPLC measurements

The seasonal variation of phytoplankton in an eutrophic tropical reservoir was evaluated through photosynthetic pigments analyzed by HPLC. The contributions of algal classes to total chlorophyll a (TChl-a) were estimated by two procedures. The first one used fixed marker pigment/chlorophyll a ratio available from culture studies of the major species of each class. In the second procedure, a matrix factorization program (CHEMTAX) was used to analyze the pigment data. The pigment data were compared with carbon biomass estimated from microscope analysis. A significant correlation between total chlorophyll a (measured by HPLC) and total biomass was obtained, indicating only a slight variation in the content of algal chlorophyll a when compared to its fluctuations in carbon biomass. The interpretation of pigment data with CHEMTAX resulted in a good agreement with biomass. Although displaying some differences, the general pattern of the phytoplankton community dynamics and the major shifts in composition, biomass and the cyanobacterial bloom were evidenced. In contrast, Chl-a biomass estimates from fixed Xan/Chl-a ratios presented poor agreement with microscope data and did not register the principal changes in phytoplankton. Our results also highlighted the needs of better understanding of the relationships between marker pigments, chlorophyll-a and algal biomass.     

Feeding Ecology of Guerezas in the Kakamega Forest,Kenya: The Importance of Moraceae Fruit in Their Diet

Eastern black-and-white colobus (Colobus guereza), or guerezas, have long been considered to be one of the most folivorous primates. I conducted a study of the feeding ecology of two guereza groups (T and O) over an annual cycle in the Kakamega Forest of western Kenya. I found that the annual diets of both groups comprised mostly of leaves (T: 48%, O: 57%) though fruit (T: 44%, O: 33%) also accounted for a substantial portion of the diet. In the six months when fruit was most abundant, fruit consumption constituted an average of 58% of T-group's monthly diet and 42% of O-group's monthly diet. In contrast to most previous studies of colobines, in which seeds were the primary fruit item consumed, almost all of the fruit eaten by guerezas at Kakamega consisted of whole fruits. At least 72% of the whole fruits consumed by T-and O-groups were whole fruits from trees in the Moraceae family, which dominates the tree family biomass at Kakamega. Unlike at sites where guerezas consumed fruit primarily when young leaves were scarce, at Kakamega guerezas ate fruit in accordance with its availability and irrespective of the availability of young leaves. My findings demonstrate that guerezas are more dietarily flexible than was previously known, which may help to explain why the species can survive in such a wide variety of forested habitats across equatorial Africa.