The absence of alternative stable states in vegetation cover of northeastern India.

Globally, forests and savannah are shown to be alternative stable states for intermediate rainfall regimes. This has implications for how these ecosystems respond to changing rainfall conditions. However, we know little about the occurrence of alternative stable states in forest ecosystems in India. In this study, we investigate the possibility of alternative stable states in the vegetation cover of northeastern India, which is a part of the Eastern Himalaya and the Indo-Burma biodiversity hotspots. To do so, we construct the so-called state diagram, by plotting frequency distributions of vegetation cover as a function of mean annual precipitation (MAP). We use remotely sensed satellite data of the enhanced vegetation index (EVI) as a proxy for vegetation cover (at 1 km resolution). We find that EVI exhibits unimodal distribution across a wide range of MAP. Specifically, EVI increases monotonically in the range 1000-2000 mm of MAP, after which it plateaus. This range of MAP corresponds to the vegetation transitional zone (1200-3700 m), whereas MAP greater than 2000 mm covers the larger extent of the tropical forest (less than or equal to 1200 m) of northeast India. In other words, we find no evidence for alternative stable states in vegetation cover or forest states at coarser scales in northeast India.

Visual signal evolution along complementary color axes in four bird lineages.

Avian color patterns function in varied behavioral contexts, most being produced by only a handful of mechanisms including feather nanostructures and pigments. Within a clade, colors may not occupy the entire available space, and incorporating complementary colors may increase the contrast and efficacy of visual signals. Here, we describe plumage patterns in four ecologically and phylogenetically diverse bird families to test whether they possess complementary colors. We present evidence that plumage colors in each clade cluster along a line in tetrachromatic color space. Additionally, we present evidence that in three of these clades, this line contains colors on opposite sides of a line passing through the achromatic point (putatively complementary colors, presenting higher chromatic contrast). Finally, interspecific color variation over at least some regions of the body is not constrained by phylogenetic relatedness. By describing plumage patterns in four diverse lineages, we add to the growing body of literature suggesting that the diversity of bird visual signals is constrained. Further, we tentatively hypothesize that in at least some clades possessing bright colors, species-specific plumage patterns may evolve by swapping the distributions of a complementary color pair. Further research on other bird clades may help confirm whether these patterns are general across bird families.

Inferring critical thresholds of ecosystem transitions from spatial data.

Ecosystems can undergo abrupt transitions between alternative stable states when the driver crosses a critical threshold. Dynamical systems theory shows that when ecosystems approach the point of loss of stability associated with these transitions, they take a long time to recover from perturbations, a phenomenon known as critical slowing down. This generic feature of dynamical systems can offer early warning signals of abrupt transitions. However, these signals are qualitative and cannot quantify the thresholds of drivers at which transition may occur. Here, we propose a method to estimate critical thresholds from spatial data. We show that two spatial metrics, spatial variance and autocorrelation of ecosystem state variable, computed along driver gradients can be used to estimate critical thresholds. First, we investigate cellular-automaton models of ecosystem dynamics that show a transition from a high-density state to a bare state. Our models show that critical thresholds can be estimated as the ecosystem state and the driver values at which spatial variance and spatial autocorrelation of the ecosystem state are maximum. Next, to demonstrate the application of the method, we choose remotely sensed vegetation data (Enhanced Vegetation Index, EVI) from regions in central Africa and northeast Australia that exhibit alternative states in woody cover. We draw transects (8 × 90 km) that span alternative stable states along rainfall gradients. Our analyses of spatial variance and autocorrelation of EVI along transects yield estimates of critical thresholds. These estimates match reasonably well with those obtained by an independent method that uses large-scale (250 × 200 km) spatial data sets. Given the generality of the principles that underlie our method, our method can be applied to a variety of ecosystems that exhibit alternative stable states.

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.

Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine.  Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause.

Divergent morphological and acoustic traits in sympatric communities of Asian barbets.

The opposing effects of environmental filtering and competitive interactions may influence community assembly and coexistence of related species. Competition, both in the domain of ecological resources, and in the sensory domain (for example, acoustic interference) may also result in sympatric species evolving divergent traits and niches. Delineating these scenarios within communities requires understanding trait distributions and phylogenetic structure within the community, as well as patterns of trait evolution. We report that sympatric assemblages of Asian barbets (frugivorous canopy birds) consist of a random phylogenetic sample of species, but are divergent in both morphological and acoustic traits. Additionally, we find that morphology is more divergent than expected under Brownian evolution, whereas vocal frequency evolution is close to the pattern expected under Brownian motion (i.e. a random walk). Together, these patterns are consistent with a role for competition or competitive exclusion in driving community assembly. Phylogenetic patterns of morphological divergence between related species suggest that these traits are key in species coexistence. Because vocal frequency and size are correlated in barbets, we therefore hypothesize that frequency differences between sympatric barbets are a by-product of their divergent morphologies.

Higher speciation and lower extinction rates influence mammal diversity gradients in Asia.

BACKGROUND: Little is known about the patterns and correlates of mammal diversity gradients in Asia. In this study, we examine patterns of species distributions and phylogenetic diversity in Asia and investigate if the observed diversity patterns are associated with differences in diversification rates between the tropical and non-tropical regions. We used species distribution maps and phylogenetic trees to generate species and phylogenetic diversity measures for 1° × 1° cells across mainland Asia. We constructed lineage-through-time plots and estimated diversification shift-times to examine the temporal patterns of diversifications across orders. Finally, we tested if the observed gradients in Asia could be associated with geographical differences in diversification rates across the tropical and non-tropical biomes. We estimated speciation, extinction and dispersal rates across these two regions for mammals, both globally and for Asian mammals. RESULTS: Our results demonstrate strong latitudinal and longitudinal gradients of species and phylogenetic diversity with Southeast Asia and the Himalayas showing highest diversity. Importantly, our results demonstrate that differences in diversification (speciation, extinction and dispersal) rates between the tropical and the non-tropical biomes influence the observed diversity gradients globally and in Asia. For the first time, we demonstrate that Asian tropics act as both cradles and museums of mammalian diversity. CONCLUSIONS: Temporal and spatial variation in diversification rates across different lineages of mammals is an important correlate of species diversity gradients observed in Asia.

Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India.

BACKGROUND: Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. METHODOLOGY/PRINCIPAL FINDINGS: We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST) of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. CONCLUSIONS/SIGNIFICANCE: Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.