Human–wildlife conflict in the roof of the world: Understanding multidimensional perspectives through a systematic review

Human–wildlife conflicts have intensified by many folds and at different levels in recent years. The same is true in the case of the Hindu Kush Himalaya (HKH), the roof of the world, and a region known for its wealth in biodiversity. We present a systematic literature review (SLR) using the search, appraisal, synthesis, and analysis (SALSA) framework; and for spatial and network analysis, we employed the VOSviewer software. The review—covering 240 peer—articles within a span of 27 years (from 1982 to 2019)—revealed that in the last decade, there was a 57% increase in publications but with a disproportionate geographical and thematic focus. About 82% of the research concentrated on protected areas and large carnivores and mega herbivores played a big role in such conflicts. About 53% of the studies were based on questionnaires, and the main driver reported was habitat disturbance of animals due to land‐cover change, urbanization, and increase in human population. On the management front, the studies reported the use of traditional protection techniques like guarding and fencing. Our analysis of 681 keywords revealed a prominent focus on ‘human‐wildlife conflict,’ ‘Nepal,’ ‘Bhutan,’ ‘Snow Leopard,’ and ‘Leopard’ indicating the issue linked with these species and countries. The involvement of 640 authors from 36 countries indicates increasing interest, and Nepal and India are playing key roles in the region. As for the spatial analysis that was conducted, while it showed regional variations, there were conspicuous limitations in terms of having a transboundary focus. Thus, particular attention ought to be paid to building transboundary partnerships and improving management interventions; there is also a pressing need to understand the patterns of human–wildlife convergence, especially involving meso‐mammals.     

Factors determining the modes of tree death in three Bornean rain forests

Abstract. Mode of tree death in relation to topography was examined in three lowland rain forests; Belalong and Andalau, in Brunei Darussalam and Danum, in Sabah, East Malaysia. In total, 1543 dead trees ≥20 cm diameter at breast height (DBH) were enumerated in an area of 36 ha. In Belalong, 31% of the dead trees had died standing, 26% had snapped, 21% had uprooted, 19% had either died‐standing or snapped and 3% remained undetermined (n = 436). In Andalau, 46% had died standing, 11% had snapped, 14% had uprooted, 26% had either died standing or snapped and 3% remained undetermined (n = 591). In Danum, 37% had died standing, 22% had snapped, 14% had uprooted, 24% had either died‐standing or snapped and 3% remained undetermined (n = 516). Slope position, e.g. whether the tree was located in a valley, mid‐slope, upper slope or ridge, was related to mode of death in all three sites. Elevation and tree diameter were related in two of the sites, and drainage, soil depth and soil shear strength were related in one of the sites. Generally the proportion of standing deaths increased moving from the valleys up to the ridge tops while uprooting proportions had the converse relationship. Slope position had little effect on the proportions of snapped trees. The three modes of death create different types of gaps. The findings substantiate that different topographies have different proportions of these gap types. The predominant gap type may have consequences for local and regional differences in forest structure and composition.     

Distribution of Indel lengths

Protein sequence alignment has become a widely used method in the study of newly sequenced proteins. Most sequence alignment methods use an affine gap penalty to assign scores to insertions and deletions. Although affine gap penalties represent the relative ease of extending a gap compared with initializing a gap, it is still an obvious oversimplification of the real processes that occur during sequence evolution. To improve the efficiency of sequence alignment methods and to obtain a better understanding of the process of sequence evolution, we wanted to find a more accurate model of insertions and deletions in homologous proteins. In this work, we extract the probability of a gap occurrence and the resulting gap length distribution in distantly related proteins (sequence identity < 25%) using alignments based on their common structures. We observe a distribution of gaps that can be fitted with a multiexponential with four distinct components. The results suggest new approaches to modeling insertions and deletions in sequence alignments.     

Overstorey Control of Understorey Species Composition in a Near-natural Temperate Broadleaved Forest in Denmark

Little is known about the importance of the forest overstorey relative to other factors in controlling the spatial variability in understorey species composition in near-natural temperate broadleaved forests. We addressed this question for the 19 ha ancient forest Suserup Skov (55°22′ N, 11°34′ E) in Denmark, one of the few old-growth temperate broadleaved forest remnants in north-western Europe, by inventorying understorey species composition and environmental conditions in 163 100 m² plots. We use unconstrained and constrained ordinations, variation partitioning, and Indicator Species Analysis to provide a quantitative assessment of the importance of the forest overstorey in controlling understorey species composition. Comparison of the gradients extracted by unconstrained and constrained ordinations showed that the main gradients in understorey species composition in our old-growth temperate broadleaved forest remnant are not caused by variability in the forest overstorey, but are related to topography and soil, edge effects, and unknown broad-scale factors. Nevertheless, overstorey-related variables uniquely accounted for 15% of the total explained variation in understorey species composition, with the pure overstorey-related (R_po), topography and soil (R_pt), edge and anthropogenic disturbance effects (R_pa), and spatial (R_ps) variation fractions being of equal magnitude. The forward variable selection showed that among the overstorey-related variables understorey light availability and to a lesser extent vertical forest structure were most important for understorey species composition. No unique influence of overstorey tree species identity could be documented. There were many indicator species for high understorey light levels and canopy gap centres, but none for medium or low light or closed canopy. Hence, no understorey species behaved as obligate shade plants. Our study shows that, the forest overstorey has a weak control of understorey species composition in near-natural broadleaved forest, in contrast to results from natural and managed forests comprising both conifer and broadleaved species. Nevertheless, >20% of the understorey species found were indicators of high light conditions or canopy openings. Hence, variability in canopy structure and understorey light availability is important for maintaining understorey species diversity.     

Species delimitation of Chinese hop‐hornbeams based on molecular and morphological evidence

Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop‐hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments (trnH–psbA, trnL–trnF, rps16, and trnG) and the nuclear internal transcribed spacer (ITS) region for all samples. Sequence variations of Ostrya from four cpDNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses‐based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop‐hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants.     

TopBP1-mediated DNA processing during mitosis

Maintenance of genome integrity is crucial to avoid cancer and other genetic diseases. Thus faced with DNA damage, cells mount a DNA damage response to avoid genome instability. The DNA damage response is partially inhibited during mitosis presumably to avoid erroneous processing of the segregating chromosomes. Yet our recent study shows that TopBP1-mediated DNA processing during mitosis is highly important to reduce transmission of DNA damage to daughter cells.¹ Pedersen RT, Kruse T, Nilsson J, Oestergaard VH, Lisby M. TopBP1 is required at mitosis to reduce transmission of DNA damage to G1 daughter cells. J Cell Biol 2015; 210:565-82; PMID:26283799; http://dx.doi.org/10.1083/jcb.201502107[Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Here we provide an overview of the DNA damage response and DNA repair during mitosis. One role of TopBP1 during mitosis is to stimulate unscheduled DNA synthesis at underreplicated regions. We speculated that such genomic regions are likely to hold stalled replication forks or post-replicative gaps, which become the substrate for DNA synthesis upon entry into mitosis. Thus, we addressed whether the translesion pathways for fork restart or post-replicative gap filling are required for unscheduled DNA synthesis in mitosis. Using genetics in the avian DT40 cell line, we provide evidence that unscheduled DNA synthesis in mitosis does not require the translesion synthesis scaffold factor Rev1 or PCNA ubiquitylation at K164, which serve to recruit translesion polymerases to stalled forks. In line with this finding, translesion polymerase η foci do not colocalize with TopBP1 or FANCD2 in mitosis. Taken together, we conclude that TopBP1 promotes unscheduled DNA synthesis in mitosis independently of the examined translesion polymerases.     

绒毛细胞与新生儿脐带血和成人外周血染色体断裂和裂隙的比较

绒毛用直接法制片,新生儿脐带血和成人外周血用半微量全血法制片。对绒毛、脐带血和外周血染色体的断裂和裂隙进行比较。结果表明,绒毛细胞的染色体断裂和裂隙比新生儿脐带血和成人外周血的显著增高,而新生儿脐带血和成人外周血之间则无明显差异。 Abstract:Chromosome breaks and gaps in chorionic villus cells and lymphocytes from newborn and abult were compared.The number of chromosome breaks and gaps in chorionic villus cells was higher than that in newborn and adult lymphocytes,This might be one of the reasons for higher chromosome aberration rate in chorionic villus.     

Effect of treefall gaps on the patchiness and species richness of Neotropical ant assemblages

Natural formation of treefall gaps plays an integral role in the ecological and evolutionary dynamics of many tropical forests, affecting the spatiotemporal distribution of plants and the animals that interact with them. This study examines the impact of treefall gaps on the spatial and temporal patchiness of ant assemblages in a moist lowland forest in Panama. Using pitfall traps and honey baits, we compared ant assemblages in five 1 to 2-year-old treefall gaps (ca 100 m²) and five adjacent plots (ca 100 m²) in undisturbed forest understory at three different times of year (late wet season, late dry season, and early wet season). We found little evidence that ant assemblages respond dramatically to the formation of treefall gaps and the differences in habitat qualities they produce. Ant abundance, species richness, species composition, and rates of resource discovery did not differ between gaps and forest understory. However, we did find significant differences in numerical abundance related to forest stratum (ground vs vegetation) and resource type in pitfall traps (oil-cockroach vs honey), and significant differences in ant species richness and rates of resource discovery across seasons. While habitat effects by themselves were never statistically significant, habitat and seasonal differences in species richness interacted significantly to produce complex, season-dependent differences among gap and forest habitats. These results suggest that the formation of natural treefall gaps has less of an effect on Neotropical ant assemblages compared to other groups of organisms (e.g., plants, birds) or other causes of patchiness (e.g., ant mosaics, moisture availability, army ant predation). The results of our study also have important implications for the underlying causes of habitat differences in the distribution of ant-defended plants. Received: 3 February 1998 / Accepted: 7 April 1998     

Finding flexible patterns in unaligned protein sequences.

We present a new method for the identification of conserved patterns in a set of unaligned related protein sequences. It is able to discover patterns of a quite general form, allowing for both ambiguous positions and for variable length wildcard regions. It allows the user to define a class of patterns (e.g., the degree of ambiguity allowed and the length and number of gaps), and the method is then guaranteed to find the conserved patterns in this class scoring highest according to a significance measure defined. Identified patterns may be refined using one of two new algorithms. We present a new (nonstatistical) significance measure for flexible patterns. The method is shown to recover known motifs for PROSITE families and is also applied to some recently described families from the literature.     

Leaf dynamics of seedlings of rain forest species in relation to canopy gaps

Summary Leaf dynamics of eight tropical rain forest species seedlings was studied in three environments: the shaded forest understorey, a small gap of ±50 m², and a large gap of ±500 m². Leaf production rate and leaf loss rate were enhanced in gaps, and a large gap resulted in larger increases than a small gap. For most species net leaf gain rate was larger in gaps, although this rate was not always largest in the large gap. Leaf loss decreased, and leaf survival percentages increased with increasing shade tolerance of species, indicating a slower leaf turnover for more shade tolerant species. Leaf area growth rate was only partly determined by net leaf gain rate. Ontogenetic effects on leaf size were also important, especially in the large gap. Species which possessed leaves with high specific leaf weight (SLW) showed lower leaf loss rates and higher leaf survival percentages than species with low SLW leaves. Leaf life span seemed to be related to leafcost per unit area. The relation of specific patterns in leaf production and leaf loss to the regeneration mode of the species is briefly discussed.