And yet it shrinks: A novel method for correcting bias in forest tree growth estimates caused by water-induced fluctuations

Accuracy in tree woody growth estimates is important to global carbon budget estimation and climate-change science. Tree growth in permanent sampling plots (PSPs) is commonly estimated by measuring stem diameter changes, but this method is susceptible to bias resulting from water-induced reversible stem shrinkage. In the absence of bias correction, temporal variability in growth is likely to be overestimated and incorrectly attributed to fluctuations in resource availability, especially in forests with high seasonal and inter-annual variability in water. We propose and test a novel approach for estimating and correcting this bias at the community level. In a 50-ha PSP from a seasonally dry tropical forest in southern India, where tape measurements have been taken every four years from 1988 to 2012, for nine trees we estimated bias due to reversible stem shrinkage as the difference between woody growth measured using tree rings and that estimated from tape. We tested if the bias estimated from these trees could be used as a proxy to correct bias in tape-based growth estimates at the PSP scale. We observed significant shrinkage-related bias in the growth estimates of the nine trees in some censuses. This bias was strongly linearly related to tape-based growth estimates at the level of the PSP, and could be used as a proxy. After bias was corrected, the temporal variance in growth rates of the PSP decreased, while the effect of exceptionally dry or wet periods was retained, indicating that at least a part of the temporal variability arose from reversible shrinkage-related bias. We also suggest that the efficacy of the bias correction could be improved by measuring the proxy on trees that belong to different size classes and census timing, but not necessarily to different species. Our approach allows for reanalysis - and possible reinterpretation of temporal trends in tree growth, above ground biomass change, or carbon fluxes in forests, and their relationships with resource availability in the context of climate change. (C) 2014 Elsevier B.V. All rights reserved.

Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation

Background. Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH) 1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. Methods. Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. Results. Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. Conclusions. Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation.

Molecules support morphology: species status of South Indian populations of the widely distributed Hanuman langur

The taxonomy of the Hanuman langur (Semnopithecus spp.), a widely distributed Asian colobine monkey, has been in a flux for a long time due to much disagreement between various classification schemes. However, results from a recent field-based morphological study were consistent with Hill's (Ceylon J Sci 21:277-305, 1939) species level classification scheme. Here we tested the validity of S. hypoleucos and S. priam, the two South Indian species recognized by Hill. To this end, one mitochondrial and four nuclear markers were sequenced from over 72 non-invasive samples of Hanuman langurs and S. johnii collected from across India. The molecular data were subjected to various tree building methods. The nuclear data was also used in a Bayesian structure analysis and to determine the genealogical sorting index of each hypothesized species. Results from nuclear data suggest that the South Indian population of Hanuman langur consists of two units that correspond to the species recognized by Hill. However in the mitochondrial tree S. johnii and S. priam were polyphyletic probably due to retention of ancestral polymorphism and/or low levels of hybridization. Implications of these results on conservation of Hanuman langurs are also discussed.

A robust layer adapted difference method for singularly perturbed two-parameter parabolic problems

A finite difference method for a time-dependent singularly perturbed convection-diffusion-reaction problem involving two small parameters in one space dimension is considered. We use the classical implicit Euler method for time discretization and upwind scheme on the Shishkin-Bakhvalov mesh for spatial discretization. The method is analysed for convergence and is shown to be uniform with respect to both the perturbation parameters. The use of the Shishkin-Bakhvalov mesh gives first-order convergence unlike the Shishkin mesh where convergence is deteriorated due to the presence of a logarithmic factor. Numerical results are presented to validate the theoretical estimates obtained.

Revalidation of Natrix clerki Wall, 1925, an overlooked species in the genus Amphiesma Dumeril, Bibron & Dumeril, 1854 (Squamata: Natricidae)

Natrix clerki Wall, 1925, previously known from its sole holotype and considered a synonym of Amphiesma parallelum (Boulenger, 1890), is resurrected in the genus Amphiesma on the basis of the analysis of morphological variation in 28 specimens of ``Amphiesma parallelum'' auctorum, plus six living, unvouchered specimens discovered in Arunachal Pradesh and Nagaland, India, and one vouchered specimen from Talle Valley in Arunachal Pradesh. Specimens from northeast India (Nagaland), northern Myanmar, and China (Yunnan), previously identified as Amphiesma parallelum either in the literature or in museum's catalogues, are also here referred to A. clerki. The holotype of Amphiesma clerki is redescribed. As a consequence, the definition of Amphiesma parallelum is modified. A. parallelum inhabits the Khasi Hills and Naga Hills in Northeast India, whereas A. clerki has a wider range in the Eastern Himalayas, northern Myanmar and Yunnan (China). Amphiesma clerki differs from A. parallelum by its longer tail, dorsal scales more strongly keeled, scales of the first dorsal scale row strongly keeled vs. smooth, a postocular streak not interrupted at the level of the neck, and a much more vivid pattern on a darker background colour. Characters of species of the Amphiesma parallelum group, i.e. A. clerki, A. parallelum, A. bitaeniatum, A. platyceps and A. sieboldii are compared. A key to this group is provided.

Impacts of climate change and management responses in tropical forests depend on complex frugivore-mediated seed dispersal

AimBiodiversity outcomes under global change will be influenced by a range of ecological processes, and these processes are increasingly being considered in models of biodiversity change. However, the level of model complexity required to adequately account for important ecological processes often remains unclear. Here we assess how considering realistically complex frugivore-mediated seed dispersal influences the projected climate change outcomes for plant diversity in the Australian Wet Tropics (all 4313 species). LocationThe Australian Wet Tropics, Queensland, Australia. MethodsWe applied a metacommunity model (M-SET) to project biodiversity outcomes using seed dispersal models that varied in complexity, combined with alternative climate change scenarios and habitat restoration scenarios. ResultsWe found that the complexity of the dispersal model had a larger effect on projected biodiversity outcomes than did dramatically different climate change scenarios. Applying a simple dispersal model that ignored spatial, temporal and taxonomic variation due to frugivore-mediated seed dispersal underestimated the reduction in the area of occurrence of plant species under climate change and overestimated the loss of diversity in fragmented tropical forest remnants. The complexity of the dispersal model also changed the habitat restoration approach identified as the best for promoting persistence of biodiversity under climate change. Main conclusionsThe consideration of complex processes such as frugivore-mediated seed dispersal can make an important difference in how we understand and respond to the influence of climate change on biodiversity.

Construction of Singer Subgroup Orbit Codes Based on Cyclic Difference Sets

A recent approach for the construction of constant dimension subspace codes, designed for error correction in random networks, is to consider the codes as orbits of suitable subgroups of the general linear group. In particular, a cyclic orbit code is the orbit of a cyclic subgroup. Hence a possible method to construct large cyclic orbit codes with a given minimum subspace distance is to select a subspace such that the orbit of the Singer subgroup satisfies the distance constraint. In this paper we propose a method where some basic properties of difference sets are employed to select such a subspace, thereby providing a systematic way of constructing cyclic orbit codes with specified parameters. We also present an explicit example of such a construction.

An estimate of the number of tropical tree species

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between similar to 40,000 and similar to 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of similar to 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of similar to 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

1. Host-parasite interactions have the potential to influence broadscale ecological and evolutionary processes, levels of endemism, divergence patterns and distributions in host populations. Understanding the mechanisms involved requires identification of the factors that shape parasite distribution and prevalence. 2. A lack of comparative information on community-level host-parasite associations limits our understanding of the role of parasites in host population divergence processes. Avian malaria (haemosporidian) parasites in bird communities offer a tractable model system to examine the potential for pathogens to influence evolutionary processes in natural host populations. 3. Using cytochrome b variation, we characterized phylogenetic diversity and prevalence of two genera of avian haemosporidian parasites, Plasmodium and Haemoproteus, and analysed biogeographic patterns of lineages across islands and avian hosts, in southern Melanesian bird communities to identify factors that explain patterns of infection. 4. Plasmodium spp. displayed isolation-by-distance effects, a significant amount of genetic variation distributed among islands but insignificant amounts among host species and families, and strong local island effects with respect to prevalence. Haemoproteus spp. did not display isolation-by-distance patterns, showed marked structuring of genetic variation among avian host species and families, and significant host species prevalence patterns. 5. These differences suggest that Plasmodium spp. infection patterns were shaped by geography and the abiotic environment, whereas Haemoproteus spp. infection patterns were shaped predominantly by host associations. Heterogeneity in the complement and prevalence of parasite lineages infecting local bird communities likely exposes host species to a mosaic of spatially divergent disease selection pressures across their naturally fragmented distributions in southern Melanesia. Host associations for Haemoproteus spp. indicate a capacity for the formation of locally co-adapted host-parasite relationships, a feature that may limit intraspecific gene flow or range expansions of closely related host species.

Systematic status of Fejervarya ((Amphibia, Anura, Dicroglossidae) from South and SE Asia with the description of a new species from the Western Ghats of Peninsular India

We carried out a large-scale phylogenetic analysis of fejervaryan (dicroglossid frogs with `Fejervaryan lines' on the ventral side of the body) frogs, distributed in South and SE Asia, using published and newly generated sequences of unidentified individuals from the northern Western Ghats. The results corroborate the presence of a larger fejervaryan clade with a sister relationship to a clade composed of Sphaerotheca. Two sister clades could be discerned within the lager fejervaryan clade. The unidentified individuals formed a monophyletic group and showed a strong support for a sister relationship with Minervarya sahyadris. The species was found to be highly divergent (16S rRNA-4% and tyr-1%) from its sister lineage Minervarya sahyadris, and the clade composed of these two lineages were found to be deeply nested within the larger clade of Fejervarya. Based on this, the genus Minervarya Dubois, Ohler and Biju, 2001 is synonymized under the genus Fejervarya Bolkay, 1915. The unidentified lineage is recognized, based on phylogenetic position, genetic divergence and morphological divergence, as a distinct species and named here as Fejervarya gomantaki sp. nov. The presence of rictal glands was observed to be a synapomorphic character shared by the nested clade members, Fejervarya sahyadris and Fejervarya gomantaki sp. nov. Based on the presence of rictal gland and small size, Minervarya chilapata, a species from a lowland region in the Eastern Himalayas, is synonymized under Fejervarya and evidence for morphological separation from the new species, Fejervarya gomantaki sp. nov. is provided. For the fejervaryan frogs, currently three generic names (Frost, 2015) are available for the two phylogenetic subclades; the genus Fejervarya Bolkay, 1915 for the species of fejervaryan frogs having distribution in the South East Asia; the genus Zakerana Howlader, 2011 for the species of fejervaryan frogs having distribution in the South Asia and the genus Minervarya Dubois, Ohler and Biju, 2001 nested within the `Zakerana clade'. In the phylogenetic analysis Minervarya sahyadris, the new species described herein as Fejervarya gomantaki sp. nov. are nested within the `Zakerana clade', if the `Zakerana clade' for the fejervaryan frogs having distribution in the South Asia is provided a generic status the nomen `Minervarya' should be considered as per the principle of priority of the ICZN Code. Taking into consideration the overlapping distribution ranges of members of the sister clades within the larger fejervaryan clade and the absence of distinct morphological characteristics, we also synonymize the genus Zakerana Howlader, 2011, a name assigned to one of the sister clades with members predominantly distributed in South Asia, under the genus Fejervarya Bolkay, 1915. We discuss the need for additional sampling to identify additional taxa and determine the geographical ranges of the members of the sister clades within Fejervarya to resolve taxonomy within this group.

Two new species of Gomphonema (Bacillariophyceae) from Doon Valley, Uttarakhand, India

This paper describes two new Gomphonema species from the lesser Himalayas, India, with their valve morphology using light and scanning electron microscopy. The two species, Gomphonema juettnerii sp. nov. and G. doonensis sp. nov., were found in Nalota stream in Doon Valley of Uttarakhand State. Main features of G. juettnerii are valve outline, shape of the areolae and striae pattern and presence of stigma. Main features of G. doonensis are rounded headpole, striae made by doubly punctate striae and features in central area. A detailed discussion on doubly punctate striae in members of gomphonemoid diatoms is presented.

Does size matter? Comparative population genetics of two butterflies with different wingspans

The dispersal ability of a species is central to its biology, affecting other processes like local adaptation, population and community dynamics, and genetic structure. Among the intrinsic, species-specific factors that affect dispersal ability in butterflies, wingspan was recently shown to explain a high amount of variance in dispersal ability. In this study, a comparative approach was adopted to test whether a difference in wingspan translates into a difference in population genetic structure. Two closely related butterfly species from subfamily Satyrinae, family Nymphalidae, which are similar with respect to all traits that affect dispersal ability except for wingspan, were studied. Melanitis leda (wingspan 60-80 mm) and Ypthima baldus (wingspan 30-40 mm) were collected from the same areas along the Western Ghats of southern India. Amplified fragment length polymorphisms were used to test whether the species with a higher wingspan (M. leda) exhibited a more homogenous population genetic structure, as compared to a species with a shorter wingspan (Y. baldus). In all analyses, Y. baldus exhibited greater degree of population genetic structuring. This study is one of the few adopting a comparative approach to establish the relationship between traits that affect dispersal ability and population genetic structure.

Morphological and functional characterisation of the burrow systems of six earthworm species (Lumbricidae)

Earthworm burrow systems are generally described based on postulated behaviours associated with the three ecological types. In this study, we used X-ray tomography to obtain 3D information on the burrowing behaviour of six very common anecic (Aporrectodea nocturna and Lumbricus terrestris) and endogeic (Aporrectodea rosea, Allolobophora chlorotica, Aporrectodea caliginosa, Aporrectodea icterica) earthworm species, introduced into repacked soil cores for 6 weeks. A simple water infiltration test, the Beerkan method, was also used to assess some functional properties of these burrow systems. Endogeic worms make larger burrow systems, which are more highly branched, less continuous and of smaller diameter, than those of anecic worms. Among the anecic species, L. terrestris burrow systems are shorter (9.2 vs 21.2 m) with a higher number (14.5 vs 23.5) of less branched burrows (12.2 vs 20.2 branches m(-1)), which are also wider (7.78 vs 5.16 mm) than those of A. nocturna. In comparison, the burrow systems made by endogeic species appeared similar to each other. However, A. rosea burrows were short and narrow, whereas A. icterica had a longer burrow system (15.7 m), more intense bioturbation intensity (refilled macropores or soil lateral compaction around them) and thus a greater number of burrows. Regarding water infiltration, anecic burrow systems were far more efficient due to open burrows linking the top and bottom of the cores. For endogeic species, we observed a linear relationship between burrow length and the water infiltration rate (R (2) = 0.49, p < 0.01). Overall, the three main characteristics significantly influencing water infiltration were burrow length, burrow number and bioturbation volume. This last characteristic highlighted the effect of burrow refilling by casts.

The interface makes a difference: lanthanide ion coated vesicles hydrolyze phosphodiesters

Lanthanide ions are strong Lewis acids. Their complexation to a variety of ligands can further enhance their Lewis acidity allowing the hydrolysis of phosphoesters and even DNA. We show that the interaction of lanthanide ions with vesicles from zwitterionic phosphatidylcholine lipids gives supramolecular structures in which the metal ion is loosely coordinated to the surface. This assembly provides a high density of Lewis-acidic metal centres, which hydrolyze phosphodiesters with enhanced rates.

A rapid method to assess reactive oxygen species in yeast using H2DCF-DA

A protocol to efficiently assess Reactive Oxygen Species (ROS) levels in yeast cells using H2DCF-DA is described here. This method employs lithium acetate to permeate the cell wall, and thus, augments the release of the fluorescent product, dichlorofluorescein from the cells. This protocol obviates the need for both physical and enzymatic lysis methods that are arduous and time consuming. This method is simple, less time consuming and reproducible, especially while dealing with a large sample size. The lithium acetate method gave significantly reproducible and linear results (P < 0.0001), as compared with direct measurement (P = 0.0005), sonication (P = 0.1466) and bead beating (P = 0.0028).