A new species of Raorchestes (Amphibia: Anura: Rhacophoridae) from mid-elevation evergreen forests of the southern Western Ghats, India

A new species of the shrub frog genus Raorchestes Biju, Souche, Dubois, Dutta and Bossuyt is described as Raorchestes kakachi sp. nov. from Agastyamalai hill region in the southern Western Ghats, India. The small sized Raorchestes (male: 24.7–25.8 mm, n = 3 and female: 24.3–34.1 mm, n = 3) is distinguished from all other known congeners by the following suite of characters. Snout oval in dorsal view; tympanum indistinct; head wider than long; moderate webbing in feet; colour on dorsum varying from ivory to brown, blotches of dark brown on flanks, brown mottling on throat reducing towards vent; inner and outer surface of thigh, inner surface of shank and inner surface of tarsus with a distinct dark brown horizontal band which extends upto first three toes on upper surface. A detailed description, advertisement call features, ecology, natural history notes and comparison with closely related species are provided for the new species.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.

Performance of established native seedlings in relation to invasive Lantana camara, rainfall and species' habitat preferences in a seasonally dry tropical forest

Native species' response to the presence of invasive species is context specific. This response cannot be studied in isolation from the prevailing environmental stresses in invaded habitats such as seasonal drought. We investigated the combined effects of an invasive shrub Lantana camara L. (lantana), seasonal rainfall and species' microsite preferences on the growth and survival of 1,105 naturally established seedlings of native trees and shrubs in a seasonally dry tropical forest. Individuals were followed from April 2008 to February 2010, and growth and survival measured in relation to lantana density, seasonality of rainfall and species characteristics in a 50-ha permanent forest plot located in Mudumalai, southern India. We used a mixed effects modelling approach to examine seedling growth and generalized linear models to examine seedling survival. The overall relative height growth rate of established seedlings was found to be very low irrespective of the presence or absence of dense lantana. 22-month growth rate of dry forest species was lower under dense lantana while moist forest species were not affected by the presence of lantana thickets. 4-month growth rates of all species increased with increasing inter-census rainfall. Community results may be influenced by responses of the most abundant species, Catunaregam spinosa, whose growth rates were always lower under dense lantana. Overall seedling survival was high, increased with increasing rainfall and was higher for species with dry forest preference than for species with moist forest preference. The high survival rates of naturally established seedlings combined with their basal sprouting ability in this forest could enable the persistence of woody species in the face of invasive species.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.

Network properties of decoys and CASP predicted models: a comparison with native protein structures

Protein structure space is believed to consist of a finite set of discrete folds, unlike the protein sequence space which is astronomically large, indicating that proteins from the available sequence space are likely to adopt one of the many folds already observed. In spite of extensive sequence-structure correlation data, protein structure prediction still remains an open question with researchers having tried different approaches (experimental as well as computational). One of the challenges of protein structure prediction is to identify the native protein structures from a milieu of decoys/models. In this work, a rigorous investigation of Protein Structure Networks (PSNs) has been performed to detect native structures from decoys/ models. Ninety four parameters obtained from network studies have been optimally combined with Support Vector Machines (SVM) to derive a general metric to distinguish decoys/models from the native protein structures with an accuracy of 94.11%. Recently, for the first time in the literature we had shown that PSN has the capability to distinguish native proteins from decoys. A major difference between the present work and the previous study is to explore the transition profiles at different strengths of non-covalent interactions and SVM has indeed identified this as an important parameter. Additionally, the SVM trained algorithm is also applied to the recent CASP10 predicted models. The novelty of the network approach is that it is based on general network properties of native protein structures and that a given model can be assessed independent of any reference structure. Thus, the approach presented in this paper can be valuable in validating the predicted structures. A web-server has been developed for this purpose and is freely available at http://vishgraph.mbu.iisc.ernet.in/GraProStr/PSN-QA.html.

Multispecies coexistence of trees in tropical forests: spatial signals of topographic niche differentiation increase with environmental heterogeneity

Neutral and niche theories give contrasting explanations for the maintenance of tropical tree species diversity. Both have some empirical support, but methods to disentangle their effects have not yet been developed. We applied a statistical measure of spatial structure to data from 14 large tropical forest plots to test a prediction of niche theory that is incompatible with neutral theory: that species in heterogeneous environments should separate out in space according to their niche preferences. We chose plots across a range of topographic heterogeneity, and tested whether pairwise spatial associations among species were more variable in more heterogeneous sites. We found strong support for this prediction, based on a strong positive relationship between variance in the spatial structure of species pairs and topographic heterogeneity across sites. We interpret this pattern as evidence of pervasive niche differentiation, which increases in importance with increasing environmental heterogeneity.

Lizard Wears Shades. A Spectacled Sphenomorphus (Squamata: Scincidae), from the Sacred Forests of Mawphlang, Meghalaya, North-east India

A new species of lygosomatine scincid lizard is described from the sacred forests of Mawphlang, in Meghalaya, northeastern India. Sphenomorphus apalpebratus sp. nov. possesses a spectacle or brille, an unusual feature within the Scincidae, and a first for the paraphyletic genus Sphenomorphus. The new species is compared with other members of the genus to which it is here assigned, as well as to members of the lygosomatine genera Lipinia and Scincella from mainland India, the Andaman and Nicobar Islands, and south-east Asia, to which it also bears resemblance. The new taxon is diagnosable in exhibiting the following combination of characters: small body size (SVL to 42.0 mm); moveable eyelids absent; auricular opening scaleless, situated in a shallow depression; dorsal scales show a line of demarcation along posterior edge of ventral pes; midbody scale rows 27-28; longitudinal scale rows between parietals and base of tail 62-64; lamellae under toe IV 8-9; supraoculars five; supralabials 5-6; infralabials 4-5; subcaudals 92; and dorsum golden brown, except at dorsal margin of lateral line, which is lighter, with four faintly spotted lines, two along each side of vertebral row of scales, that extend to tail base. The new species differs from its congeners in the lack of moveable eyelids, a character shared with several distantly related scincid genera.

Scale-dependent relationships between tree species richness and ecosystem function in forests

1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which represent a majority of global biomass, productivity and biodiversity. 2. Here, we conduct an analysis of relationships between tree species richness, biomass and productivity in 25 forest plots of area 8-50ha from across the world. The data were collected using standardized protocols, obviating the need to correct for methodological differences that plague many studies on this topic. 3. We found that at very small spatial grains (0.04ha) species richness was generally positively related to productivity and biomass within plots, with a doubling of species richness corresponding to an average 48% increase in productivity and 53% increase in biomass. At larger spatial grains (0.25ha, 1ha), results were mixed, with negative relationships becoming more common. The results were qualitatively similar but much weaker when we controlled for stem density: at the 0.04ha spatial grain, a doubling of species richness corresponded to a 5% increase in productivity and 7% increase in biomass. Productivity and biomass were themselves almost always positively related at all spatial grains. 4. Synthesis. This is the first cross-site study of the effect of tree species richness on forest biomass and productivity that systematically varies spatial grain within a controlled methodology. The scale-dependent results are consistent with theoretical models in which sampling effects and niche complementarity dominate at small scales, while environmental gradients drive patterns at large scales. Our study shows that the relationship of tree species richness with biomass and productivity changes qualitatively when moving from scales typical of forest surveys (0.04ha) to slightly larger scales (0.25 and 1ha). This needs to be recognized in forest conservation policy and management.

Challenges in vulnerability assessment of forests under climate change

Forest-management goals in the context of climate change are to reduce the adverse impact of climate change on biodiversity, ecosystem services and carbon stocks. For developing an effective adaptation strategy, knowledge on nature and sources of vulnerability of forests is necessary to conserve or enhance carbon sinks. However, assessing the vulnerability of forest ecosystems is a challenging task, as the mechanisms that determine vulnerability cannot be observed directly. In this article, we list the challenges in forest vulnerability assessments and propose an assessment of inherent vulnerability by using process-based indicators under the current climate. We also suggest periodic assessment of vulnerability, which is necessary to review adaptation strategies for the management of forests and forest carbon stocks.

Product Dimension of Forests and Bounded Treewidth Graphs

The product dimension of a graph G is defined as the minimum natural number l such that G is an induced subgraph of a direct product of l complete graphs. In this paper we study the product dimension of forests, bounded treewidth graphs and k-degenerate graphs. We show that every forest on n vertices has product dimension at most 1.441 log n + 3. This improves the best known upper bound of 3 log n for the same due to Poljak and Pultr. The technique used in arriving at the above bound is extended and combined with a well-known result on the existence of orthogonal Latin squares to show that every graph on n vertices with treewidth at most t has product dimension at most (t + 2) (log n + 1). We also show that every k-degenerate graph on n vertices has product dimension at most inverted right perpendicular5.545 k log ninverted left perpendicular + 1. This improves the upper bound of 32 k log n for the same by Eaton and Rodl.

Long-Term Environmental Correlates of Invasion by Lantana camara (Verbenaceae) in a Seasonally Dry Tropical Forest

Invasive species, local plant communities and invaded ecosystems change over space and time. Quantifying this change may lead to a better understanding of the ecology and the effective management of invasive species. We used data on density of the highly invasive shrub Lantana camara (lantana) for the period 1990-2008 from a 50 ha permanent plot in a seasonally dry tropical forest of Mudumalai in southern India. We used a cumulative link mixed-effects regression approach to model the transition of lantana from one qualitative density state to another as a function of biotic factors such as indicators of competition from local species (lantana itself, perennial grasses, invasive Chromolaena odorata, the native shrub Helicteres isora and basal area of native trees) and abiotic factors such as fire frequency, inter-annual variability of rainfall and relative soil moisture. The density of lantana increased substantially during the study period. Lantana density was negatively associated with the density of H. isora, positively associated with basal area of native trees, but not affected by the presence of grasses or other invasive species. In the absence of fire, lantana density increased with increasing rainfall. When fires occurred, transitions to higher densities occurred at low rainfall values. In drier regions, lantana changed from low to high density as rainfall increased while in wetter regions of the plot, lantana persisted in the dense category irrespective of rainfall. Lantana seems to effectively utilize resources distributed in space and time to its advantage, thus outcompeting local species and maintaining a population that is not yet self-limiting. High-risk areas and years could potentially be identified based on inferences from this study for facilitating management of lantana in tropical dry forests.

Identifying Priority Areas for Conservation and Management in Diverse Tropical Forests

The high concentration of the world's species in tropical forests endows these systems with particular importance for retaining global biodiversity, yet it also presents significant challenges for ecology and conservation science. The vast number of rare and yet to be discovered species restricts the applicability of species-level modelling for tropical forests, while the capacity of community classification approaches to identify priorities for conservation and management is also limited. Here we assessed the degree to which macroecological modelling can overcome shortfalls in our knowledge of biodiversity in tropical forests and help identify priority areas for their conservation and management. We used 527 plant community survey plots in the Australian Wet Tropics to generate models and predictions of species richness, compositional dissimilarity, and community composition for all the 4,313 vascular plant species recorded across the region (>1.3 million communities (grid cells)). We then applied these predictions to identify areas of tropical forest likely to contain the greatest concentration of species, rare species, endemic species and primitive angiosperm families. Synthesising these alternative attributes of diversity into a single index of conservation value, we identified two areas within the Australian wet tropics that should be a high priority for future conservation actions: the Atherton Tablelands and Daintree rainforest. Our findings demonstrate the value of macroecological modelling in identifying priority areas for conservation and management actions within highly diverse systems, such as tropical forests.

Stabilizing the Native Trimer of HIV-1 Env by Destabilizing the Heterodimeric Interface of the gp41 Postfusion Six-Helix Bundle

The HIV-1 envelope glycoprotein (Env) is a trimer of gp120-gp41 heterodimers and is essential for viral entry. The gp41 subunit in native, prefusion trimeric Env exists in a metastable conformation and attains a stable six-helix bundle (6-HB) conformation comprised of a trimer of N-heptad repeat (NHR) and C-heptad repeat (CHR) heterodimers, that drives the fusion of viral and cellular membranes. We attempted to stabilize native Env trimers by incorporation of mutations at the NHR-CHR interface that disrupt the postfusion 6-HB of gp41. The mutations V570D and I573D stabilize native Env of the HIV-1 JRFL strain and occlude nonneutralizing epitopes to a greater extent than the previously identified I559P mutation that is at the interface of the NHR trimers in the 6-HB. The mutations prevent soluble-CD4 (sCD4)-induced gp120 shedding and 6-HB formation. In the context of cell surface-expressed JRFL Env, introduction of a previously reported additional disulfide between residues A501 and T605 perturbs the native conformation, though this effect is partially alleviated by furin coexpression. The data suggest that positions 570 and 573 are surface proximal in native Env and that the NHR homotrimeric coiled coil in native Env terminates before or close to residue 573. Aspartic acid substitutions at these positions stabilize native trimers through destabilization of the postfusion 6-HB conformation. These mutations can be used to stabilize Env in a DNA vaccine format. IMPORTANCE The major protein on the surface of HIV-1 is the envelope (Env) glycoprotein. Env is a trimer of gp120-gp41 heterodimers. gp120 is involved in receptor/coreceptor binding and gp41 in the fusion of viral and cellular membranes. Like many other viral fusion proteins, the gp41 subunit in native trimeric Env exists in a metastable conformation. gp41 readily forms a stable six-helix bundle (6-HB) conformation comprised of a trimer of N-heptad repeat (NHR) and C-heptad repeat (CHR) heterodimers that drives fusion of viral and cellular membranes. While it is expected that native Env is a good immunogen, its metastability results in exposure of immunodominant nonneutralizing epitopes. In the present study, we stabilize native Env trimers by incorporation of a number of different mutations at the NHR-CHR interface that disrupt the postfusion 6-HB of gp41. The stabilized constructs described here can be incorporated into DNA vaccine candidates.

Community-managed forests and wildlife-friendly agriculture play a subsidiary but not substitutive role to protected areas for the endangered Asian elephant

Global conservation policy is increasingly debating the feasibility of reconciling wildlife conservation and human resource requirements in land uses outside protected areas (PAs). However, there are few quantitative assessments of whether or to what extent these `wildlife-friendly' land uses fulfill a fundamental function of PAs-to separate biodiversity from anthropogenic threats. We distinguish the role of wildlife-friendly land uses as being (a) subsidiary, whereby they augment PAs with secondary habitat, or (b) substitutive, wherein they provide comparable habitat to PAs. We tested our hypotheses by investigating the influence of land use and human presence on space-use intensity of the endangered Asian elephant (Elephas maximus) in a fragmented landscape comprising PAs and wildlife-friendly land uses. We applied multistate occupancy models to spatial data on elephant occurrence to estimate and model the overall probability of elephants using a site, and the conditional probability of high-intensity use given that elephants use a site. The probability of elephants using a site regardless of intensity did not vary between PAs and wildlife-friendly land uses. However, high-intensity use declined with distance to PM, and this effect was accentuated by an increase in village density. Therefore, while wildlife-friendly land uses did play a subsidiary conservation role, their potential to substitute for PAs was offset by a strong human presence. Our findings demonstrate the need to evaluate the role of wildlife-friendly land uses in landscape-scale conservation; for species that have conflicting resource requirements with people, PAs are likely to provide crucial refuge from growing anthropogenic threats. (C) 2014 Elsevier Ltd. All rights reserved.