Effects of habitat disturbance and food supply on population densities of three primate species in the Kakamega Forest, Kenya

While habitat disturbance and food availability are major factors thought to determine the abundance of primates, evidence for their importance is uneven. We assessed the effects of these factors on three monkey species, guerezas ( Colobus guereza ) , blue monkeys ( Cercopithecus mitis ) and redtails ( Cercopithecus ascanius ), in four areas of the Kakamega Forest, Kenya. Group densities of guerezas and blue monkeys were higher in areas where disturbance levels were also higher. Food availability measured as basal area density of food trees did not correlate significantly with the group densities of any of the three monkeys. The diversity of food trees, another potential measure of food abundance did, however, correlate with group densities of guerezas and blue monkeys suggesting that food availability may positively influence monkey density, and may sometimes increase with disturbance. Group densities of redtails did not correlate with any habitat variable examined, suggesting that factors other than those we considered may have influenced the abundance of this species particularly.     

Forest structure and biomass in post-agricultural forests: Lessons learned with new spatial tools

Questions: With calls for afforestation to sequester carbon due to climate change, agricultural land will be converted to forests in the near future. Little is known about how the ecosystem services of reforested landscapes with an agricultural land-use history will differ from reference forests. Our objectives were to (i) test the hypothesis that forests with a history of agricultural land use can provide the same carbon storage and biomass ecosystem services as adjacent reference forests, given some recovery time; (ii) explore whether there is a lag in the recovery of forest community composition due to prior agricultural land use; and (iii) demonstrate how remote-sensing methods can improve our understanding of land-use legacies at large spatial scales. Location: Finger Lakes National Forest, NY, USA. Methods: Using historic air photos, landscape-scale lidar, and field surveys, we compared differences in biomass storage, forest structure, and vegetation communities between reference forests and post-agricultural forests at different stages of regeneration in the Finger Lakes National Forest, New York, USA. We also used lidar to create a spatial model of biomass across the landscape to analyze the spatial distribution of biomass across our study area. Results: We found biomass and forest structure in post-agricultural forests generally recovered to levels typical of reference forests within 50 years of abandonment. Conversely, we found the composition of woody and herbaceous communities still varied between reference and post-agricultural forests after 50 years of abandonment. Conclusions: Collectively our results indicate afforestation efforts can be effective for carbon sequestration at early stages of forest succession. Our spatial model of biomass indicated that biomass levels can be low in forests with extensive edge. Further research is needed to understand how contemporary landscape structure interacts with legacy effects of agriculture to affect biomass and other ecosystem services.     

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.     

Assessment of census techniques for interspecific comparisons of tropical rainforest bird densities: a field evaluation in the Western Ghats, India

Studies comparing different bird censusing methods are useful for assessing relative biases, synthesizing data across studies, and designing bird population monitoring programmes. A field study was carried out in mid-elevation tropical rainforest in the Western Ghats to compare bird density estimates from line transect, point count and territory spot-mapping methods. Interspecific comparisons were made using data for 13 common resident bird species, including two endemics. Variable-width line transect density estimates were highly correlated with, but slightly (17%) higher than, those produced by territory spot-mapping. Although densities from variable-width point counts and spot-mapping were highly positively correlated, the estimates were 95% higher on average in the former. Higher density estimates relative to spot-mapping were produced mainly for the most abundant species, probably due to their mobility and the inclusion of additional individuals that enter the count area during the count period. Fixed-width strip transects and point counts produced density estimates that were highly correlated with, but significantly lower than, variable-width estimates. Wherever possible, territory spot-mapping and line transects are recommended for density estimates; the former may yield additional information on spatial distribution of birds. Fixed-width transects or point counts, being easier to apply, may be used for large-scale monitoring programmes. Interspecific variation in flocking systems and the poor visibility in dense rainforest vegetation indicate the need for care in collection of data on flock size and its variation, which is necessary for estimating the density of individuals. The variation across methods suggests the need for further research using multiple methods across years and marked individuals to verify territoriality and accuracy.     

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.     

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.     

Estimating densities of large herbivores in tropical forests: Rigorous evaluation of a dung‐based method

When sighting‐based surveys to estimate population densities of large herbivores in tropical dense forests are not practical or affordable, surveys that rely on animal dung are sometimes used. This study tested one such dung‐based method by deriving population densities from observed dung densities of six large herbivores (chital, elephant, gaur, muntjac, sambar, and wild pig) in two habitats, dry deciduous forests (DDF) and moist deciduous forests (MDF), within Nagarahole National Park, southern India. Using the program DUNGSURV, dung pile counts, decay rates estimated from field experiments, and defecation rates derived from literature were analyzed together by a model that allows for random events affecting dung decay. Densities of chital were the highest, followed by sambar. Wild pig densities were similar in the two habitats, sambar densities were higher in DDF, and densities of the other species were higher in MDF than in DDF. We compared DUNGSURV estimates with densities estimated using distance sampling in the same season. DUNGSURV estimates were substantially higher for all species in both habitats. These differences highlight the challenges that researchers face in computing unbiased estimates of dung decay rates and in relying on defecation rates from literature. Besides the elephant, this study is the first to rigorously test the efficacy of using a dung‐based approach to estimate densities of large herbivore species in Asia, and based on this evaluation, we provide specific recommendations to address issues that require careful consideration before observed dung densities are used to derive animal densities. Our results underline the need for an experimental study of a known population in a fenced reserve to validate the true potential of using dung‐based approaches to estimate population densities.     

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.     

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.     

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.     

Forest aboveground biomass along an elevational transect in Sulawesi,Indonesia, and the role of Fagaceae in tropical montane rain forests

Aim This study investigates how estimated tree aboveground biomass (AGB) of tropical montane rain forests varies with elevation, and how this variation is related to elevational change in floristic composition, phylogenetic community structure and the biogeography of the dominant tree taxa. Location Lore Lindu National Park, Sulawesi, Indonesia. Methods Floristic inventories and stand structural analyses were conducted on 13 plots (each 0.24 ha) in four old‐growth forest stands at 1050, 1400, 1800 and 2400 m a.s.l. (submontane to upper montane elevations). Tree AGB estimates were based on d.b.h., height and wood specific gravity. Phylogenetic diversity and biogeographical patterns were analysed based on tree family composition weighted by AGB. Elevational trends in AGB were compared with other Southeast Asian and Neotropical transect studies (n = 7). Results AGB was invariant from sub‐ to mid‐montane elevation (309–301 Mg ha^?1) and increased slightly to 323 Mg ha^?1 at upper montane elevation. While tree and canopy height decreased, wood specific gravity increased. Magnoliids accounted for most of the AGB at submontane elevations, while eurosids I (including Fagaceae) contributed substantially to AGB at all elevations. Phylogenetic diversity was highest at upper montane elevations, with co‐dominance of tree ferns, Podocarpaceae, Trimeniaceae and asterids/euasterids II, and was lowest at lower/mid‐montane elevations, where Fagaceae contributed > 50% of AGB. Biogeographical patterns showed a progression from dominant tropical families at submontane to tropical Fagaceae (Castanopsis, Lithocarpus) at lower/mid‐montane, and to conifers and Australasian endemics at upper montane elevations. Cross‐continental comparisons revealed an elevational AGB decrease in transects with low/no presence of Fagaceae, but relatively high AGB in montane forests with moderate to high abundance of this family. Main conclusions AGB is determined by both changes in forest structure and shifts in species composition. In our study, these two factors traded off so that there was no net change in AGB, even though there were large changes in forest structure and composition along the elevational gradient. Southeast Asian montane rain forests dominated by Fagaceae constitute important carbon stocks. The importance of biogeography and species traits for biomass estimation should be considered by initiatives to reduce emissions from deforestation and forest degradation (REDD) and in taxon choice in reforestation for carbon offsetting.     

Evaluating the suitability of planted forests for African forest monkeys: a case study from Kakamega forest, Kenya

As natural forest cover declines, planted forests have come to occupy an increasing percentage of the earth's surface, yet we know little about their suitability as alternative habitat for wildlife. Although some primate species use planted forests, few studies have compared primate populations in natural and nearby planted forests. From March 2006 to July 2010, we conducted line transect surveys and assessed group sizes and compositions in natural and nearby 60-70 year old mixed indigenous planted forest to determine the densities of diurnal primate species (Colobus guereza, Cercopithecus mitis, C. ascanius) in these two forest types at Isecheno, Kakamega Forest, Kenya. Line transect data were analyzed using the Encounter Rate, Whitesides, and Distance sampling methods, which all provided broadly consistent results. We found that all three diurnal primate species occupy both natural and planted forest at Isecheno. However, group densities of the two Cercopithecus species were 42-46% lower in planted than in natural forest. Colobus guereza achieved comparable group densities in the two forest types, although the species is found in smaller groups, and thus at lower (35%) individual density, in planted than in natural forest. Following a logging episode in the planted forest mid-way through our study, Cercopithecus ascanius group densities fell by 60% while C. mitis and Colobus guereza group densities remained stable over the next two years. Overall, our results suggest that while primate species vary in their response to habitat disturbance, planted forest has the potential to contribute to the conservation of some African monkey species. Even for the relatively flexible taxa in our study, however, 60-70 year old mixed indigenous planted forest failed to support densities comparable to those in nearby natural forest. From the perspective of Kakamega's primates, planted forests may supplement natural forest, but are not an adequate replacement for it.     

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.     

Growth and biomass productivity of Scenedesmus vacuolatus on a twin layer system and a comparison with other types of cultivations

Scenedesmus is a genus of microalgae employed for several industrial uses. Industrial cultivations are performed in open ponds or in closed photobioreactors (PBRs). In the last years, a novel type of PBR based on immobilized microalgae has been developed termed porous substrate photobioreactors (PSBR) to achieve significant higher biomass density during cultivation in comparison to classical PBRs. This work presents a study of the growth of Scenedesmus vacuolatus in a Twin Layer System PSBR at different light intensities (600 μmol photons m⁻² s⁻¹ or 1000 μmol photons m⁻² s⁻¹), different types and concentrations of the nitrogen sources (nitrate or urea), and at two CO₂ levels in the gas phase (2% or 0.04% v/v). The microalgal growth was followed by monitoring the attached biomass density as dry weight, the specific growth rate and pigment accumulation. The highest productivity (29 g m⁻² d⁻¹) was observed at a light intensity of 600 μmol photons m⁻² s⁻¹ and 2% CO₂. The types and concentrations of nitrogen sources did not influence the biomass productivity. Instead, the higher light intensity of 1000 μmol photons m⁻² s⁻¹ and an ambient CO₂ concentration (0.04%) resulted in a significant decrease of productivity to 18 and 10–12 g m⁻² d⁻¹, respectively. When compared to the performance of similar cultivation systems (15–30 g m⁻² d⁻¹), these results indicate that the Twin Layer cultivation System is a competitive technique for intensified microalgal cultivation in terms of productivity and, at the same time, biomass density.