Monsoon Regimes and Processes in CCSM4. Part I: The Asian-Australian Monsoon

The simulation characteristics of the Asian-Australian monsoon are documented for the Community Climate System Model, version 4 (CCSM4). This is the first part of a two part series examining monsoon regimes in the global tropics in the CCSM4. Comparisons are made to an Atmospheric Model Intercomparison Project (AMIP) simulation of the atmospheric component in CCSM4 Community Atmosphere Model, version 4, (CAM4)] to deduce differences in the monsoon simulations run with observed sea surface temperatures (SSTs) and with ocean-atmosphere coupling. These simulations are also compared to a previous version of the model (CCSM3) to evaluate progress. In general, monsoon rainfall is too heavy in the uncoupled AMIP run with CAM4, and monsoon rainfall amounts are generally better simulated with ocean coupling in CCSM4. Most aspects of the Asian-Australian monsoon simulations are improved in CCSM4 compared to CCSM3. There is a reduction of the systematic error of rainfall over the tropical Indian Ocean for the South Asian monsoon, and well-simulated connections between SSTs in the Bay of Bengal and regional South Asian monsoon precipitation. The pattern of rainfall in the Australian monsoon is closer to observations in part because of contributions from the improvements of the Indonesian Throughflow and diapycnal diffusion in CCSM4. Intraseasonal variability of the Asian-Australian monsoon is much improved in CCSM4 compared to CCSM3 both in terms of eastward and northward propagation characteristics, though it is still somewhat weaker than observed. An improved simulation of El Nino in CCSM4 contributes to more realistic connections between the Asian-Australian monsoon and El Nino-Southern Oscillation (ENSO), though there is considerable decadal and century time scale variability of the strength of the monsoon-ENSO connection.

Variation at Diabetes- and Obesity-Associated Loci May Mirror Neutral Patterns of Human Population Diversity and Diabetes Prevalence in India

South Asian populations harbor a high degree of genetic diversity, due in part to demographic history. Two studies on genome-wide variation in Indian populations have shown that most Indian populations show varying degrees of admixture between ancestral north Indian and ancestral south Indian components. As a result of this structure, genetic variation in India appears to follow a geographic cline. Similarly, Indian populations seem to show detectable differences in diabetes and obesity prevalence between different geographic regions of the country. We tested the hypothesis that genetic variation at diabetes-and obesity-associated loci may be potentially related to different genetic ancestries. We genotyped 2977 individuals from 61 populations across India for 18 SNPs in genes implicated in T2D and obesity. We examined patterns of variation in allele frequency across different geographical gradients and considered state of origin and language affiliation. Our results show that most of the 18 SNPs show no significant correlation with latitude, the geographic cline reported in previous studies, or by language family. Exceptions include KCNQ1 with latitude and THADA and JAK1 with language, which suggests that genetic variation at previously ascertained diabetes-associated loci may only partly mirror geographic patterns of genome-wide diversity in Indian populations.

In the elephant's seed shadow: the prospects of domestic bovids as replacement dispersers of three tropical Asian trees

As populations of the world's largest animal species decline, it is unclear how ecosystems will react to their local extirpation. Due to the unique ecological characteristics of megaherbivores such as elephants, seed dispersal is one ecosystem process that may be affected as populations of large animals are decimated. In typically disturbed South Asian ecosystems, domestic bovids (cattle, Bos primigenius, and buffalo, Bubalus bubalis) may often be the species most available to replace Asian elephants (Elephas maximus) as endozoochorous dispersers of large-fruited mammal-dispersed species. We use feeding trials, germination trials, and movement data from the tropical moist forests of Buxa Tiger Reserve (India) to examine whether domestic bovids are viable replacements for elephants in the dispersal of three largefruited species: Dillenia indica, Artocarpus chaplasha, and Careya arborea. We find that (1) once consumed, seeds are between 2.5 (C. arborea) and 26.5 (D. indica) times more likely to pass undigested into elephant dung than domestic bovid dung; and (2) seeds from elephant dung germinated as well as or better than seeds taken from bovid dung for all plant species, with D. indica seeds from elephant dung 1.5 times more likely to germinate. Furthermore, since wild elephants have less constrained movements than even free-roaming domestic bovids, we calculate that maximum dispersal by elephants is between 9.5 and 11.2 times farther than that of domestic bovids, with about 20% of elephant-dispersed seeds being moved farther than the maximum distance seeds are moved by bovids. Our findings suggest that, while bovids are able to disperse substantial numbers of seeds over moderate distances for two of the three study species, domestic bovids will be unable to routinely emulate the reliable, long-distance dispersal of seeds executed by elephants in this tropical moist forest. Thus while domestic bovids can attenuate the effects of losing elephants as dispersers, they may not be able to prevent the decline of various mammal-dispersed fruiting species in the face of overhunting, habitat fragmentation, and climate change.

Warm pool thermodynamics from the Arabian Sea Monsoon Experiment (ARMEX)

Before the onset of the south Asian summer monsoon, sea surface temperature (SST) of the north Indian Ocean warms to 30–32°C. Climatological mean mixed layer depth in spring (March–May) is 10–20 m, and net surface heat flux (Q net ) is 80–100 W m−2 into the ocean. Previous work suggests that observed spring SST warming is small mainly because of (1) penetrative flux of solar radiation through the base of the mixed layer (Q pen ) and (2) advective cooling by upper ocean currents. We estimate the role of these two processes in SST evolution from a two-week Arabian Sea Monsoon Experiment process experiment in April–May 2005 in the southeastern Arabian Sea. The upper ocean is stratified by salinity and temperature, and mixed layer depth is shallow (6 to 12 m). Current speed at 2 m depth is high even under light winds. Currents within the mixed layer are quite distinct from those at 25 m. On subseasonal scales, SST warming is followed by rapid cooling, although the ocean gains heat at the surface: Q net is about 105 W m−2 in the warming phase and 25 W m−2 in the cooling phase; penetrative loss Q pen is 80 W m−2 and 70 W m−2. In the warming phase, SST rises mainly because of heat absorbed within the mixed layer, i.e., Q net minus Q pen ; Q pen reduces the rate of SST warming by a factor of 3. In the second phase, SST cools rapidly because (1) Q pen is larger than Q net and (2) advective cooling is ∼85 W m−2. A calculation using time-averaged heat fluxes and mixed layer depth suggests that diurnal variability of fluxes and upper ocean stratification tends to warm SST on subseasonal timescale. Buoy and satellite data suggest that a typical premonsoon intraseasonal cooling event occurs under clear skies when the ocean is gaining heat through the surface. In this respect, premonsoon SST cooling in the north Indian Ocean is different from that due to the Madden-Julian oscillation or monsoon intraseasonal oscillation.

Intraseasonal response of mixed layer temperature and salinity in the Bay of Bengal to heat and freshwater flux

Buoy and satellite data show pronounced subseasonal oscillations of sea surface temperature (SST) in the summertime Bay of Bengal. The SST oscillations are forced mainly by surface heat flux associated with the active break cycle of the south Asian summer monsoon. The input of freshwater (FW) from summer rain and rivers to the bay is large, but not much is known about subseasonal salinity variability. We use 2002-2007 observations from three Argo floats with 5 day repeat cycle to study the subseasonal response of temperature and salinity to surface heat and freshwater flux in the central Bay of Bengal. About 95% of Argo profiles show a shallow halocline, with substantial variability of mixed layer salinity. Estimates of surface heat and freshwater flux are based on daily satellite data sampled along the float trajectory. We find that intraseasonal variability of mixed layer temperature is mainly a response to net surface heat flux minus penetrative radiation during the summer monsoon season. In winter and spring, however, temperature variability appears to be mainly due to lateral advection rather than local heat flux. Variability of mixed layer freshwater content is generally independent of local surface flux (precipitation minus evaporation) in all seasons. There are occasions when intense monsoon rainfall leads to local freshening, but these are rare. Large fluctuations in FW appear to be due to advection, suggesting that freshwater from rivers and rain moves in eddies or filaments.

The Skill of ECMWF Medium-Range Forecasts during the Year of Tropical Convection 2008

This study uses the European Centre for Medium-Range Weather Forecasts (ECMWF) model-generated high-resolution 10-day-long predictions for the Year of Tropical Convection (YOTC) 2008. Precipitation forecast skills of the model over the tropics are evaluated against the Tropical Rainfall Measuring Mission (TRMM) estimates. It has been shown that the model was able to capture the monthly to seasonal mean features of tropical convection reasonably. Northward propagation of convective bands over the Bay of Bengal was also forecasted realistically up to 5 days in advance, including the onset phase of the monsoon during the first half of June 2008. However, large errors exist in the daily datasets especially for longer lead times over smaller domains. For shorter lead times (less than 4-5 days), forecast errors are much smaller over the oceans than over land. Moreover, the rate of increase of errors with lead time is rapid over the oceans and is confined to the regions where observed precipitation shows large day-to-day variability. It has been shown that this rapid growth of errors over the oceans is related to the spatial pattern of near-surface air temperature. This is probably due to the one-way air-sea interaction in the atmosphere-only model used for forecasting. While the prescribed surface temperature over the oceans remain realistic at shorter lead times, the pattern and hence the gradient of the surface temperature is not altered with change in atmospheric parameters at longer lead times. It has also been shown that the ECMWF model had considerable difficulties in forecasting very low and very heavy intensity of precipitation over South Asia. The model has too few grids with ``zero'' precipitation and heavy (>40 mm day(-1)) precipitation. On the other hand, drizzle-like precipitation is too frequent in the model compared to that in the TRMM datasets. Further analysis shows that a major source of error in the ECMWF precipitation forecasts is the diurnal cycle over the South Asian monsoon region. The peak intensity of precipitation in the model forecasts over land (ocean) appear about 6 (9) h earlier than that in the observations. Moreover, the amplitude of the diurnal cycle is much higher in the model forecasts compared to that in the TRMM estimates. It has been seen that the phase error of the diurnal cycle increases with forecast lead time. The error in monthly mean 3-hourly precipitation forecasts is about 2-4 times of the error in the daily mean datasets. Thus, effort should be given to improve the phase and amplitude forecast of the diurnal cycle of precipitation from the model.

Woody plant seedling distribution under invasive Lantana camara thickets in a dry-forest plot in Mudumalai, southern India

Lantana camara, a shrub of Central and South American origin, has become invasive across dry forests worldwide. The effect of the thicket-forming habit of L. camara as a dispersal and recruitment barrier in a community of native woody seedlings was examined in a 50-ha permanent plot located in the seasonally dry forest of Mudumalai, southern India. Sixty 100-m(2) plots were enumerated for native woody seedlings between 10-100 cm in height. Of these, 30 plots had no L. camara thickets, while the other 30 had dense thickets. The frequency of occurrence and abundance of seedlings were modelled as a function of dispersal mode (mammal, bird or mechanical) and affinities to forest habitats (dry forest, moist forest or ubiquitous) as well as presence or absence of dense L. camara thickets. Furthermore, frequency of occurrence and abundance of individual species were also compared between thickets and no L. camara. At the community level, L. camara density, dispersal mode and forest habitat affinities of species determined both frequency of occurrence and abundance of seedlings, with the abundance of dry-forest mammal-dispersed species and ubiquitous mechanically dispersed species being significantly lower under L. camara thickets. Phyllanthus emblica and Kydia calycina were found to be significantly less abundant under L. camara, whereas most other species were not affected by the presence of thickets. It was inferred that, by affecting the establishment of native tree seedlings, L. camara thickets could eventually alter the community composition of such forests.

A study of vertical cloud structure of the Indian summer monsoon using CloudSat data

Precise specification of the vertical distribution of cloud optical properties is important to reduce the uncertainty in quantifying the radiative impacts of clouds. The new global observations of vertical profiles of clouds from the CloudSat mission provide opportunities to describe cloud structures and to improve parameterization of clouds in the weather and climate prediction models. In this study, four years (2007-2010) of observations of vertical structure of clouds from the CloudSat cloud profiling radar have been used to document the mean vertical structure of clouds associated with the Indian summer monsoon (ISM) and its intra-seasonal variability. Active and break monsoon spells associated with the intra-seasonal variability of ISM have been identified by an objective criterion. For the present analysis, we considered CloudSat derived column integrated cloud liquid and ice water, and vertically profiles of cloud liquid and ice water content. Over the South Asian monsoon region, deep convective clouds with large vertical extent (up to 14 km) and large values of cloud water and ice content are observed over the north Bay of Bengal. Deep clouds with large ice water content are also observed over north Arabian Sea and adjoining northwest India, along the west coast of India and the south equatorial Indian Ocean. The active monsoon spells are characterized by enhanced deep convection over the Bay of Bengal, west coast of India and northeast Arabian Sea and suppressed convection over the equatorial Indian Ocean. Over the Bay of Bengal, cloud liquid water content and ice water content is enhanced by similar to 90 and similar to 200 % respectively during the active spells. An interesting feature associated with the active spell is the vertical tilting structure of positive CLWC and CIWC anomalies over the Arabian Sea and the Bay of Bengal, which suggests a pre-conditioning process for the northward propagation of the boreal summer intra-seasonal variability. It is also observed that during the break spells, clouds are not completely suppressed over central India. Instead, clouds with smaller vertical extent (3-5 km) are observed due to the presence of a heat low type of circulation. The present results will be useful for validating the vertical structure of clouds in weather and climate prediction models.

Effects of large-scale deforestation on precipitation in the monsoon regions: Remote versus local effects

In this paper, using idealized climate model simulations, we investigate the biogeophysical effects of large-scale deforestation on monsoon regions. We find that the remote forcing from large-scale deforestation in the northern middle and high latitudes shifts the Intertropical Convergence Zone southward. This results in a significant decrease in precipitation in the Northern Hemisphere monsoon regions (East Asia, North America, North Africa, and South Asia) and moderate precipitation increases in the Southern Hemisphere monsoon regions (South Africa, South America, and Australia). The magnitude of the monsoonal precipitation changes depends on the location of deforestation, with remote effects showing a larger influence than local effects. The South Asian Monsoon region is affected the most, with 18% decline in precipitation over India. Our results indicate that any comprehensive assessment of afforestation/reforestation as climate change mitigation strategies should carefully evaluate the remote effects on monsoonal precipitation alongside the large local impacts on temperatures.

Inter-comparison and performance evaluation of chemistry transport models over Indian region

Aerosol loading over the South Asian region has the potential to affect the monsoon rainfall, Himalayan glaciers and regional air-quality, with implications for the billions in this region. While field campaigns and network observations provide primary data, they tend to be location/season specific. Numerical models are useful to regionalize such location-specific data. Studies have shown that numerical models underestimate the aerosol scenario over the Indian region, mainly due to shortcomings related to meteorology and the emission inventories used. In this context, we have evaluated the performance of two such chemistry-transport models: WRF-Chem and SPRINTARS over an India-centric domain. The models differ in many aspects including physical domain, horizontal resolution, meteorological forcing and so on etc. Despite these differences, both the models simulated similar spatial patterns of Black Carbon (BC) mass concentration, (with a spatial correlation of 0.9 with each other), and a reasonable estimates of its concentration, though both of them under-estimated vis-a-vis the observations. While the emissions are lower (higher) in SPRINTARS (WRF-Chem), overestimation of wind parameters in WRF-Chem caused the concentration to be similar in both models. Additionally, we quantified the under-estimations of anthropogenic BC emissions in the inventories used these two models and three other widely used emission inventories. Our analysis indicates that all these emission inventories underestimate the emissions of BC over India by a factor that ranges from 1.5 to 2.9. We have also studied the model simulations of aerosol optical depth over the Indian region. The models differ significantly in simulations of AOD, with WRF-Chem having a better agreement with satellite observations of AOD as far as the spatial pattern is concerned. It is important to note that in addition to BC, dust can also contribute significantly to AOD. The models differ in simulations of the spatial pattern of mineral dust over the Indian region. We find that both meteorological forcing and emission formulation contribute to these differences. Since AOD is column integrated parameter, description of vertical profiles in both models, especially since elevated aerosol layers are often observed over Indian region, could be also a contributing factor. Additionally, differences in the prescription of the optical properties of BC between the models appear to affect the AOD simulations. We also compared simulation of sea-salt concentration in the two models and found that WRF-Chem underestimated its concentration vis-a-vis SPRINTARS. The differences in near-surface oceanic wind speeds appear to be the main source of this difference. In-spite of these differences, we note that there are similarities in their simulation of spatial patterns of various aerosol species (with each other and with observations) and hence models could be valuable tools for aerosol-related studies over the Indian region. Better estimation of emission inventories could improve aerosol-related simulations. (C) 2015 Elsevier Ltd. All rights reserved.

Genetic analysis of foot-and-mouth disease virus serotype A of Indian origin and detection of positive selection and recombination in leader protease- and capsid-coding regions

The leader protease (L-pro) and capsid-coding sequences (P1) constitute approximately 3 kb of the foot-and-mouth disease virus (FMDV). We studied the phylogenetic relationship of 46 FMDV serotype A isolates of Indian origin collected during the period 1968-2005 and also eight vaccine strains using the neighbour-joining tree and Bayesian tree methods. The viruses were categorized under three major groups - Asian, Euro-South American and European. The Indian isolates formed a distinct genetic group among the Asian isolates. The Indian isolates were further classified into different genetic subgroups (<5% divergence). Post-1995 isolates were divided into two subgroups while a few isolates which originated in the year 2005 from Andhra Pradesh formed a separate group. These isolates were closely related to the isolates of the 1970s. The FMDV isolates seem to undergo reverse mutation or onvergent evolution wherein sequences identical to the ancestors are present in the isolates in circulation. The eight vaccine strains included in the study were not related to each other and belonged to different genetic groups. Recombination was detected in the L-pro region in one isolate (A IND 20/82) and in the VP1 coding 1D region in another isolate (A RAJ 21/96). Positive selection was identified at aa positions 23 in the L-pro (P<0.05; 0.046*) and at aa 171 in the capsid protein VP1 (P<0.01; 0.003**).

Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos

Represented by approximately 85 species, Hemidactylus is one of the most diverse and widely distributed genera of reptiles in the world. In the Indian subcontinent, this genus is represented by 28 species out of which at least 13 are endemic to this region. Here, we report the phylogeny of the Indian Hemidactylus geckos based on mitochondrial and nuclear DNA markers sequenced from multiple individuals of widely distributed as well as endemic congeners of India. Results indicate that a majority of the species distributed in India form a distinct clade whose members are largely confined to the Indian subcontinent thus representing a unique Indian radiation. The remaining Hemidactylus geckos of India belong to two other geographical clades representing the Southeast Asian and West-Asian arid zone species. Additionally, the three widely distributed, commensal species (H. brookii, H. frenatus and H. flaviviridis) are nested within the Indian radiation suggesting their Indian origin. Dispersal-vicariance analysis also supports their Indian origin and subsequent dispersal out-of-India into West-Asian arid zone and Southeast Asia. Thus, Indian subcontinent has served as an important arena for diversification amongst the Hemidactylus geckos and in the evolution and spread of its commensal geckos. (C) 2010 Elsevier Inc. All rights reserved.

High P-T granulite relicts from the Imjingang belt, South Korea:Tectonic significance

This study presents a detailed description on crustal metamorphic signatures of garnet-clinopyroxene-quartz-rutile-bearing high P-T granulites, Samgot unit, Imajingang belt, northwestern Korean Peninsula that formed during Permo-Triassic regional metamorphism related to the amalgamation of East Asian continental fragments. Lenses and blocks of high P-T granulites and garnet-bearing leucosomes occur within mafic metamorphic rocks (mainly amphibolites). The mafic blocks comprise relicts of granoblastic garnet and clinopyroxene with medium-grained quartz and rutile. These relict mineral assemblages are confined to local micro-domains and constitute remnants of peak metamorphism. Plagioclase and amphibole form only as retrograde phases in medium ton coarse-grained moats that rim grain boundaries between relict peak mineral assemblages. This microstructure represents the reaction between garnet, clinopyroxene, quartz and rutile in the presence of melt to form amphibole, plagioclase and titanite with minor biotite. The leucosome domains consist of euhedral garnets within the quartz-K feldspar-plagioclase (granitic) matrix, probably representing peritectic garnet growth along with melting. The rare earth element (REE) composition of minerals also support the peritectic garnet growth with a positive Eu/Eu* (positive Eu anomaly), while the relict garnet shows a slight negative anomaly typical for high-grade granulites. The peak-metamorphic conditions calculated from thermodynamic modeling and compositional isopleths indicate a temperature around c. 900 degrees C at a pressure around c. 20 kbar. The present P-T path indicates a clear multi-stage decompression history with initial decompression and cooling followed by a stage of decompression during hydration possibly during Late Triassic exhumation. The results from this study together with the presence of eclogites from the Hongsung area suggest that the Imjingang area and the western Gyeonggi massif likely resided at crustal levels deeper than those of the eastern and southern part of the Gyeonggi massif. (C) 2009 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae)

The two recently proposed taxonomies of the langurs and leaf monkeys (Subfamily Colobinae) provide different implications to our understanding of the evolution of Nilgiri and purple-faced langurs. Groves (2001) [Groves, C.P., 2001. Primate Taxonomy. Smithsonian Institute Press, Washington], placed Nilgiri and purple-faced langurs in the genus Trachypithecus, thereby suggesting disjunct distribution of the genus Trachypithecus. [Brandon-Jones, D., Eudey, A.A., Geissmann, T., Groves, C.P., Melnick, D.J., Morales, J.C., Shekelle, M., Stewart, C.-B., 2003. Asian primate classification. Int. J. Primatol. 25, 97–162] placed these langurs in the genus Semnopithecus, which suggests convergence of morphological characters in Nilgiri and purple-faced langurs with Trachypithecus. To test these scenarios, we sequenced and analyzed the mitochondrial cytochrome b gene and two nuclear DNA-encoded genes, lysozyme and protamine P1, from a variety of colobine species. All three markers support the clustering of Nilgiri and purple-faced langurs with Hanuman langur (Semnopithecus), while leaf monkeys of Southeast Asian (Trachypithecus) form a distinct clade. The phylogenetic position of capped and golden leaf monkeys is still unresolved. It is likely that this species group might have evolved due to past hybridization between Semnopithecus and Trachypithecus clades.