Habitat occupancy of sloth bear Melursus ursinus in Chitwan National Park,Nepal

Mammals have experienced a massive decline in their populations and geographic ranges worldwide. The sloth bear, Melursus ursinus (Shaw, 1791), is one of many species facing conservation threats. Despite being endangered in Nepal, decades of inattention to the situation have hindered their conservation and management. We assessed the distribution and patterns of habitat use by sloth bears in Chitwan National Park (CNP), Nepal. We conducted sign surveys from March to June, 2020, in 4 × 4 km grids (n = 45). We collected detection/non‐detection data along a 4‐km trail that was divided into 20 continuous segments of 200 m each. We obtained environmental, ecological, and anthropogenic covariates to understand determinants of sloth bear habitat occupancy. The data were analyzed using the single‐species single‐season occupancy method, with a spatially correlated detection. Using repeated observations, these models accounted for the imperfect detectability of the species to provide robust estimates of habitat occupancy. The model‐averaged occupancy estimate for the sloth bear was 69% and the detection probability was 0.25. The probability of habitat occupancy by sloth bears increased with the presence of termites and fruits and in rugged, dry, open, undisturbed habitats. Our results indicate that the sloth bear is elusive, functionally unique, and widespread in CNP. Future conservation interventions and action plans aimed at sloth bear management must adequately consider their habitat requirements.     

生物信息学软件研究的可视化分析

以Web of Science数据库为数据来源,利用Cite Space和UCINET软件对发表在Nucleic Acids Research期刊上有关生物信息学软件研究的文献做了可视化分析,揭示了该领域的研究力量、作者团队与高被引作者、知识基础、期刊分布、研究热点与前沿,为生物信息学软件的研究和发展提供必要的参考依据。     

生物信息学数据库研究文献引文与热点分析

以Web of Science为数据源,简要概括生物信息学数据库研究的发展趋势。利用Cite Space可视化工具展现生物信息学数据库研究的知识基础和研究热点图谱,为开展生物信息学数据库领域相关的理论研究和实践活动提供借鉴,以便推动生物信息学数据库研究的发展。研究表明：1990年Altschul SF发表的＂局部比对搜索工具——BLAST＂是生物信息学数据库研究的重要知识来源文献;热点主题集中在序列库、基因组数据库、分类数据库、蛋白质数据库、数据库更新、集成系统等。     

Changes in sediment phosphate composition of seasonal ponds during filling

Most ponds from the Doñana National Park are shallow temporary freshwater bodies on eolian sands. The total phosphate concentration and the fractional P-composition of the sediments from two small ponds were studied before and inmediately after they were filled (autumn, 1996). Total phosphorus concentration was measured in 2 different size fractions: 2–0.1 mm (coarse) and <0.1 mm (fine). In both ponds, the total phosphorus concentration of the fine sediment increased by 20% at the beginning of the filling period, whereas 5 weeks later it did not increase further. The percentage of organic matter of the fine sediment was relatively high (between 13–18%) and did not change significantly during filling. The concentration of sediment total iron and Fe(OOH) increased significantly in both ponds during filling. The sequential P fractionation of the fine sediment included, besides the determination of two inorganic fractions (Ca-bound P and Fe-bound P), an organic-P fraction extracted with acid, another extracted with alkali, two organic-P fractios from the Ca-EDTA/dithionite and the Na₂-EDTA extracts which contained high concentrations of humic substances. The pond sediments were rich in organic P compounds as the sum of all organic-P fractions ranged between 267 and 320 g g^-1 (68% and 79% of the sum of all fractions). Significant changes (P<0.01) in the fractional P-composition of sediments were found after filling. Acid soluble organic phosphate increased about 30% in both ponds. Iron-bound phosphate increased significantly (about 40%) only in the pond where a higher concentration of Fe(OOH) was measured after filling. An adsorption experiment was carried out for each sediment to simulate P input during filling. Both the iron-bound phosphate and Ca-bound P increased significantly (P<0.01) suggesting that these two fractions were involved in the P-adsorption during the laboratory experiment.     

Fracture toughness of mountain gorilla (Gorilla gorilla beringei) food plants

Mountain gorillas, the largest extant primates, subsist almost entirely on plant matter. Moreover, their diet includes a substantial amount of structural material, such as bark and stems, which other primates tend to avoid. Accordingly, the robust masticatory apparatus of gorillas may be adaptive to this presumably tough diet; however, quantitative information on this subject is lacking. In this study the fracture toughness of mountain gorilla foods was examined for the first time. Samples of 44 food plants from Bwindi-Impenetrable National Park (BINP) and Mgahinga Gorilla National Park (MGNP) were tested. These parks are inhabited by two gorilla populations that regarded by some as being distinct at the subspecific taxonomic level. Although food toughness did not differ between the two populations, both diets contained tough items. Tree barks were the toughest food items (varying from 0.23 to 8.2 kJ/m2), followed by shrub barks, pith, and stems. The toughness of leaves and fruit was negligible compared to that of bark. The toughness of bamboo was low in comparison to the toughest food items. Accordingly, the prominent toughness of bark, pith, and stems may be key factors in the evolution of orofacial robusticity in mountain gorillas.     

<Emphasis Type="Italic">Thermobaculum terrenum</Emphasis> gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia

A novel bacterium was cultivated from an extreme thermal soil in Yellowstone National Park, Wyoming, USA, that at the time of sampling had a pH of 3.9 and a temperature range of 65–92 °C. This organism was found to be an obligate aerobic, non-spore-forming rod, and formed pink-colored colonies. Phylogenetic analysis of the 16S rRNA gene sequence placed this organism in a clade composed entirely of environmental clones most closely related to the phyla Chloroflexi and Thermomicrobia. This bacterium stained gram-positive, contained a novel fatty-acid profile, had cell wall muramic acid content similar to that of Bacillus subtilis (significantly greater than Escherichia coli), and failed to display a lipopolysaccharide profile in SDS-polyacrylamide gels that would be indicative of a gram-negative cell wall structure. Ultrastructure examinations with transmission electron microscopy showed a thick cell wall (approximately 34 nm wide) external to a cytoplasmic membrane. The organism was not motile under the culture conditions used, and electron microscopic examination showed no evidence of flagella. Genomic G+C content was 56.4 mol%, and growth was optimal at 67 °C and at a pH of 7.0. This organism was able to grow heterotrophically on various carbon compounds, would use only oxygen as an electron acceptor, and its growth was not affected by light. A new species of a novel genus is proposed, with YNP1^T (T=type strain) being Thermobaculum terrenum gen. nov., sp. nov. (16S rDNA gene GenBank accession AF391972). This bacterium has been deposited in the American Type Culture Collection (ATCC BAA-798) and the University of Oregon Culture Collection of Microorganisms from Extreme Environments (CCMEE 7001).     

Spatial and population genetic structure of microsatellites in white pine

We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity was high and inbreeding low. When comparing these populations, there is a significant, but small (less than 1%), genetic divergence between populations. Spatial distance between populations or timber harvest at the second growth site were reasonable explanations for the observed minor differences in allele frequencies between populations. Spatial autocorrelation analysis suggested that, for the old growth population, weak positive structuring at 15 m fits the isolation by distance model for a neighbourhood size of about 100 individuals. In comparison, genotypes were randomly distributed in the second growth population. Thus, logging may have decreased spatial structuring at the second growth site, suggesting that management practices may be used to alter natural spatial patterns. In addition, the amount of autocorrelation in the old growth population appears to be lower for some of the microsatellites, suggesting higher numbers of rare alleles and that higher mutation rates may have directly affected spatial statistics by reducing structure.     

Substrate heterogeneity and number of plant species in Everglades savannas (Florida,USA)

Environmental heterogeneity, especially that related to topography, has been proposed to influence numbers of plant species in different sized areas. Despite little variation in elevation, large numbers of vascular plant species occur in some habitats. This study explored possible relationships between number of plant species and substrateheterogeneity in two species-rich habitats, subtropical pine savannas and short-hydroperiod prairies, in the Long Pine Key region of Everglades National Park (Florida, U.S.A.). We examined relationships between numbers of vascular plant species and topographic heterogeneity by measuring numbers of species and elevations in differ-ent sizes of nested plots that spanned five orders of magnitude (0.1 m² to 1000 m² ) and that were located along two transects extending from pine savannas into short-hydroperiod prairies in different areas of Long Pine Key. We also classified substrates and soil depths in 1 m 2 sized submodules within the nested plots. Pine savannas occurred at higher elevations than adjacent short-hydroperiod prairies. Although differences occurred in substrate types and distribution within 1 m 2 plots, numbers of species were not associated with these differences. Vari-ances in elevations were similar in the smallest plots, but increased with area more rapidly in pine savannas than in short-hydroperiod prairies. Plot size explained about 85% of the variation in species numbers, which increased from 2040 per 1 m 2 to 80120 per 1000 m² . An interaction between habitat and scale explained 5% of the variation; more species occurred in shorthydroperiod prairies than pine savannas at scales <10 m² , but the re-verse occurred at scales >10 m². The number of species in pine savannas at scales of 1 m²and 10 m²was positively associated with variation in elevations; no significant relationships were obtained in short-hydroperiod prairies, which lack the fine-scale topographic variation of pine savannas. Our data indicate that substrate het-erogeneity, measured as variation in elevations, is not likely to be involved in the co-occurrence of many species within small areas of these savannas, but may influence numbers of species at larger scales of observation, es-pecially in pine savannas. Why many plant species occur within very small areas in these savannas remains un-answered.     

'Gatherings' of social grooming among wild chimpanzees: implications for evolution of sociality

Chimpanzees (Pan troglodytes) often groom in gatherings that cannot simply be divided into unilateral dyadic grooming interactions. This feature of grooming is studied at two different levels: grooming cliques and grooming clusters. Grooming cliques are defined as directly connected configurations of grooming interactions at any given moment, and when any member of a clique successively grooms any member of another clique within 5min and within a distance of 3m, all the members of both cliques are defined as being in the same grooming cluster. Twenty-seven types of cliques are observed, with the largest one consisting of seven individuals. Mutual and/or polyadic cliques account for more than 25% of all cliques. The size of grooming clusters varies from two to 23 individuals, and almost 70% of the grooming time is spent in polyadic clusters. Although adult males groom the longest in relatively smaller clusters (size=2-4), adult females groomed the longest in clusters of five or more individuals. A review of the literature implies that mutual and polyadic cliques occur less often in other primate species than in chimpanzees. The importance of overlapping interactions for these kinds of gatherings and its possible significance in the evolution of sociality is discussed in this article.     

Pollen competition in a natural population of Cucurbita foetidissima (Cucurbitaceae)

The pollen competition hypothesis predicts that when the number of pollen grains deposited onto stigmas exceeds the number of ovules, selection can operate in the time frame between deposition and fertilization. Moreover, because of the overlap in gene expression between the two phases of the life cycle, selection on microgametophytes may alter the resulting sporophytic generation. The extent to which pollen competition occurs in nature has been unclear, because tests of the predictions of the pollen competition hypothesis have used cultivars and/or artificial growth conditions and hand-pollination techniques. In this study we used a wild species, Cucurbita foetidissima, in its natural habitat (southern New Mexico) to determine the amount and timing of the arrival of pollen onto stigmas, the relationship between pollen deposition and seed number, and the effects of the intensity of pollen competition on progeny vigor. We found that ～900 pollen grains are necessary for full seed set and that a single visit by a pollinator results in the deposition of 653.0 ± 101.8 pollen grains. About 29% of the flowers receiving a single pollinator visit had 900 or more pollen grains on its stigma. Moreover, within 2 h of anthesis, >4000 pollen grains were deposited onto a typical stigma, indicating that multiple pollinator visits must have occurred. Fruits produced by multiple visits had greater seed numbers (206 vs. 147) than fruits produced by a single visit. Finally, the progeny produced by multiple pollinator visits were more vigorous than those produced by single visits with respect to five measures of vegetative growth (MANCOVA, Wilks' lambda = 0.96, F(6,370) = 2.54, P < 0.02. These data demonstrate that conditions for pollen competition exist in nature and support the prediction that pollen competition enhances offspring vigor.