@article {43846, title = {Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.}, journal = {Wellcome Open Res}, volume = {3}, year = {2019}, month = {01/2019}, pages = {44}, abstract = {

Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. 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. 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.\  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.

}, issn = {2398-502X}, doi = {10.12688/wellcomeopenres.14438.1}, author = {Dias, Mary and Pattabiraman, Chitra and Siddappa, Shilpa and Gowda, Malali and Shet, Anita and Smith, Derek and Muehlemann, Barbara and Tamma, Krishnapriya and Solomon, Tom and Jones, Terry and Krishna, Sudhir} } @article {26659, title = {Climatic and geographic barriers drive distributional patterns of bird phenotypes within peninsular India}, journal = {Journal of Avian Biology}, volume = {48}, year = {2017}, month = {05/2017}, pages = {620-630}, abstract = {

Modern phylogenetic data provide unparalleled ability to test biogeographic paradigms, often suggested by differences in species distribution patterns. However, such approaches have been applied less at regional scales, particularly in Asia. In the absence of such data, we examine if concordance of distributional patterns for phenotypes (subspecies) suggest potential biogeographic barriers for birds in peninsular India. Specifically, we examine climatic and physical factors that might limit phenotype distributions in this region.

Various physical, vegetation and climatic barriers were demarcated to identify potential biogeographic units within peninsular India. We then collated occurrence of endemic or disjunctly distributed species and subspecies within these units using published range maps. We also quantified turnover between potential units, allowing us to identify significant biogeographic barriers. Three time-step climate data (Last Glacial Maxima, mid-Holocene and present) enabled us to examine differences between these potential biogeographic regions through time.

The Palk Straits, followed by the Goa Gap (\~{} 16{\textdegree}N) and the Godavari River emerged as the major barriers in this region. The Palk Straits and Godavari are physical barriers while Goa Gap appears to be a climate-mediated ecological divide. Mountain barriers like the Palghat Gap are not the most significant barriers as previously thought. Climatically intermediate regions appeared unstable in the past and showed inconsistent affinities to different geographic units across families. We suggest that relative climatic stability of the wet regions of the southern western Ghats could be responsible for high subspecies endemism here. Our approach provides hypotheses that can be tested with comparative multi-species phylogeographic data in the future.

}, doi = {10.1111/jav.01278}, author = {Ramachandran, V and Robin, V V and Tamma, Krishnapriya and Ramakrishnan, Uma} } @article {11601, title = {Divergent morphological and acoustic traits in sympatric communities of Asian barbets.}, journal = {R Soc Open Sci}, volume = {3}, year = {2016}, month = {2016 Aug}, pages = {160117}, abstract = {

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.

}, doi = {10.1098/rsos.160117}, author = {Krishnan, Anand and Tamma, Krishnapriya} } @article {875, title = {Higher speciation and lower extinction rates influence mammal diversity gradients in Asia.}, journal = {BMC Evol Biol}, volume = {15}, year = {2015}, month = {2015}, pages = {11}, abstract = {

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{\textdegree} {\texttimes} 1{\textdegree} 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.

}, keywords = {Animals, Asia, Biodiversity, Genetic Speciation, Mammals, Phylogeny}, issn = {1471-2148}, doi = {10.1186/s12862-015-0289-1}, author = {Tamma, Krishnapriya and Ramakrishnan, Uma} }