Temporal variability of forest communities: empirical estimates of population change in 4000 tree species

Long-term surveys of entire communities of species are needed to measure fluctuations in natural populations and elucidate the mechanisms driving population dynamics and community assembly. We analysed changes in abundance of over 4000 tree species in 12 forests across the world over periods of 6-28years. Abundance fluctuations in all forests are large and consistent with population dynamics models in which temporal environmental variance plays a central role. At some sites we identify clear environmental drivers, such as fire and drought, that could underlie these patterns, but at other sites there is a need for further research to identify drivers. In addition, cross-site comparisons showed that abundance fluctuations were smaller at species-rich sites, consistent with the idea that stable environmental conditions promote higher diversity. Much community ecology theory emphasises demographic variance and niche stabilisation; we encourage the development of theory in which temporal environmental variance plays a central role.

Cryptic species and Miocene diversification of Palaearctic naked-toed geckos (Squamata: Gekkonidae) in the Indian dry zone

We sampled Palaearctic naked-toed geckos from across their range in India and used two mitochondrial and two nuclear genes to reconstruct relationships within a global phylogeny. Published sequences of Peninsular Indian Hemidactylus allow us to contrast these two groups in dating analyses - providing insights into the history of the Indian dry zone. Palaearctic naked-toed geckos first moved onto the Indian Plate in the Oligocene, with higher-level diversification probably linked to collision of the Indian and Eurasian plates, and subsequent dispersal into-India and diversification with increasing Miocene aridity. An independent gekkonid radiation with species in the dry zone, Hemidactylus diversified during the same period in Peninsular India. Our results demonstrate that dry zone taxa across India may date back to at least the Miocene, with a potential historical climatic barrier between the Indus and Peninsular Indian Divisions. `Cyrtopodion' aravallense is revealed to be a complex with seven genetically and environmentally divergent lineages that began diversifying in the late Miocene, congruent with increased aridity in north-western India. This discovery of cryptic diversity in the Indian dry zone represents the first terrestrial vertebrate radiation from north-western central India and highlights how little we understand of the regions' biodiversity, emphasizing the need for systematic geographic sampling and multiline evidence to reveal true patterns of diversity. The ancestor of `Cyrtopodion' aravallense came into the nascent Indian dry zone in the Miocene and has since diversified, potentially in the absence of any sympatric scansorial rupicolous geckos. Cyrtopodion scabrum represents a unique case of commensalism and shows phylogeographic structure in its presumed native range. The taxonomic implications of our study include a number of undescribed species, recognition of `Cyrtopodion' as a distinct lineage and the non-monophyly of Altiphylax.

Vermicompost reduces the invasiveness of the earthworm species Dichogaster bolaui compared to the use of compost in a degraded tropical soil in Northern Vietnam

In Northern Vietnam, organic fertilization programmes are being tested to restore soil fertility and reduce soil erosion. However, the amendment of organic matter in soil is also associated with the development of the invasive earthworm species Dichogaster bolaui. The objective of this study was to investigate the influence of organic matter amendment quality (compost vs. vermicompost) on D. bolaui. Our study confirmed D. bolaui development in organic patches in the field. However, we also observed that the flat-backed millipede Asiomorpha coarctata proliferated in these organic patches. Native to Asia, this millipede species is also considered as invasive in America. Both D. bolaui and A. coarctata more rapidly colonized compost than vermicompost patches. A laboratory experiment confirmed this trend and showed the limited development of D. bolaui in vermicompost. This is probably because of the decreased palatability of this substrate to soil fauna. In conclusion, any restoration practice that aims to increase the organic stocks in soils degraded by erosion should consider the quality of the organic amendment. In Northern Vietnam, vermicompost may be the preferred substrate for restoring soils while limiting the spread of D. bolaui. (C) 2014 Elsevier Masson SAS. All rights reserved.

Interferon-gamma induced cell death: Regulation and contributions of nitric oxide, cJun N-terminal kinase, reactive oxygen species and peroxynitrite

Interferon-gamma (Ifn gamma), a known immunomodulatory cytokine, regulates cell proliferation and survival. In this study, the mechanisms leading to the selective susceptibility of some tumor cells to Ifn gamma were deciphered. Seven different mouse tumor cell lines tested demonstrated upregulation of MHC class I to variable extents with Ifn gamma; however, only the cell lines, H6 hepatoma and L929 fibrosarcoma, that produce higher amounts of nitric oxide (NO) and reactive oxygen species (ROS) are sensitive to Ifn gamma-induced cell death. NO inhibitors greatly reduce Ifn gamma-induced ROS; however, ROS inhibitors did not affect the levels of Ifn gamma-induced NO, demonstrating that NO regulates ROS. Consequently, NO inhibitors are more effective, compared to ROS inhibitors, in reducing Ifn gamma-induced cell death. Further analysis revealed that Ifn gamma induces peroxynitrite and 3-nitrotyrosine amounts and a peroxynitrite scavenger, FeTPPS, reduces cell death. Ifn gamma treatment induces the phosphorylation of c-jun N-terminal kinase (Jnk) in H6 and L929 but not CT26, a colon carcinoma cell line, which is resistant to Ifn gamma-mediated death. Jnk activation downstream to NO leads to induction of ROS, peroxynitrite and cell death in response to Ifn gamma. Importantly, three cell lines tested, i.e. CT26, EL4 and Neuro2a, that are resistant to cell death with Ifn gamma alone become sensitive to the combination of Ifn gamma and NO donor or ROS inducer in a peroxynitrite-dependent manner. Overall, this study delineates the key roles of NO as the initiator and Jnk, ROS, and peroxynitrite as the effectors during Ifn gamma-mediated cell death. The implications of these findings in the Ifn gamma-mediated treatment of malignancies are discussed. (C) 2014 Elsevier B.V. All rights reserved.

Interferon-gamma induced cell death: Regulation and contributions of nitric oxide, cJun N-terminal kinase, reactive oxygen species and peroxynitrite

Interferon-gamma (Ifn gamma), a known immunomodulatory cytokine, regulates cell proliferation and survival. In this study, the mechanisms leading to the selective susceptibility of some tumor cells to Ifn gamma were deciphered. Seven different mouse tumor cell lines tested demonstrated upregulation of MHC class I to variable extents with Ifn gamma; however, only the cell lines, H6 hepatoma and L929 fibrosarcoma, that produce higher amounts of nitric oxide (NO) and reactive oxygen species (ROS) are sensitive to Ifn gamma-induced cell death. NO inhibitors greatly reduce Ifn gamma-induced ROS; however, ROS inhibitors did not affect the levels of Ifn gamma-induced NO, demonstrating that NO regulates ROS. Consequently, NO inhibitors are more effective, compared to ROS inhibitors, in reducing Ifn gamma-induced cell death. Further analysis revealed that Ifn gamma induces peroxynitrite and 3-nitrotyrosine amounts and a peroxynitrite scavenger, FeTPPS, reduces cell death. Ifn gamma treatment induces the phosphorylation of c-jun N-terminal kinase (Jnk) in H6 and L929 but not CT26, a colon carcinoma cell line, which is resistant to Ifn gamma-mediated death. Jnk activation downstream to NO leads to induction of ROS, peroxynitrite and cell death in response to Ifn gamma. Importantly, three cell lines tested, i.e. CT26, EL4 and Neuro2a, that are resistant to cell death with Ifn gamma alone become sensitive to the combination of Ifn gamma and NO donor or ROS inducer in a peroxynitrite-dependent manner. Overall, this study delineates the key roles of NO as the initiator and Jnk, ROS, and peroxynitrite as the effectors during Ifn gamma-mediated cell death. The implications of these findings in the Ifn gamma-mediated treatment of malignancies are discussed. (C) 2014 Elsevier B.V. All rights reserved.

Importance of intraspecifically gregarious species in a tropical bird community

In both single- and mixed-species social groups, certain participants are known to play important roles in providing benefits. Identifying these participants is critical for understanding group dynamics, but is often difficult with large roving social groups in the wild. Here, we develop a new approach to characterize roles in social groups and apply it to mixed-species bird flocks (flocks hereafter) in an Indian tropical evergreen forest. Two types of species, namely intraspecifically gregarious and sallying species, are thought to play important roles in flocks because studies have shown they attract other flock participants. However, it is unclear why these types are attractive and whether they are essential for flock formation. We address these questions by focusing on the composition of the subset of flocks containing only two species each. In two-species flocks, it is reasonable to assume that at least one species obtains some kind of benefit. Therefore, only those species combinations that result in benefit to at least one species should occur as two-species flocks. Using data from 540 flocks overall, of which 158 were two-species flocks, we find that intraspecifically gregarious species are disproportionately represented in two-species flocks and always lead flocks when present, and that flocks containing them are joined significantly more by other species. Our results suggest that intraspecifically gregarious species are likely to be the primary benefit providers in flocks and are important for tropical flock formation. Our study also provides a new approach to understanding importance in other mixed-species and single-species social groups.

Species and acoustic diversity of bats in a palaeotropical wet evergreen forest in southern India

The Western Ghats of India is among the top 25 biodiversity hotspots in the world. About 43% of the reported 117 bat species in India are found in this region, but few quantitative studies of bat echolocation calls and diversity have been carried out here thus far. A quantitative study of bat diversity was therefore conducted using standard techniques, including mist-netting, acoustical and roost surveys in the wet evergreen forests of Kudremukh National Park in the Western Ghats of Karnataka. A total of 106 bats were caught over 108 sampling nights, representing 17 species, 3 belonging to Megachiroptera and 14 to Microchiroptera. Acoustical and roost surveys added three more species, two from Microchiroptera and one from Megachiroptera. Of these 20 species, 4 belonged to the family Pteropodidae, 10 to Vespertilionidae, 3 to Rhinolophidae, 2 to Megadermatidae and 1 to Hipposideridae. We recorded the echolocation calls of 13 of the 16 microchiropteran species, of which the calls of 4 species (Pipistrellus coromandra, Pipistrellus affinis, Pipistrellus ceylonicus and Harpiocephalus harpia) have been recorded for the first time. Discriminant function analyses of the calls of 11 species provided 91.7% correct classification of individuals to their respective species, indicating that the echolocation calls could be used successfully for non-invasive acoustic surveys and monitoring of bat species in the future.

Lineage delimitation and description of nine new species of bush frogs (Anura: Raorchestes, Rhacophoridae) from the Western Ghats Escarpment

Bush frogs of the genus Raorchestes are distributed mainly in the Western Ghats Escarpment of Peninsular India. The inventory of species in this genus is incomplete and there is ambiguity in the systematic status of species recognized by morphological criteria. To address the dual problem of taxon sampling and systematic uncertainty in bush frogs, we used a large-scale spatial sampling design, explicitly incorporating the geographic and ecological heterogeneity of the Western Ghats. We then used a hierarchical multi-criteria approach by combining mitochondrial phylogeny, genetic distance, geographic range, morphology and advertisement call to delimit bush frog lineages. Our analyses revealed the existence of a large number of new lineages with varying levels of genetic divergence. Here, we provide diagnoses and descriptions for nine lineages that exhibit divergence across multiple axes. The discovery of new lineages that exhibit high divergence across wide ranges of elevation and across the major massifs highlights the large gaps in historical sampling. These discoveries underscore the significance of addressing inadequate knowledge of species distribution, namely the ``Wallacean shortfall'', in addressing the problem of taxon sampling and unknown diversity in tropical hotspots. A biogeographically informed sampling and analytical approach was critical in detecting and delineating lineages in a consistent manner across the genus. Through increased taxon sampling, we were also able to discern a number of well-supported sub-clades that were either unresolved or absent in earlier phylogenetic reconstructions and identify a number of shallow divergent lineages which require further examination for assessment of their taxonomic status.

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.

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.

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.

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.