On Bayesian "central clustering": Application to landscape classification of Western Ghats

Landscape classification of the well-known biodiversity hotspot, Western Ghats (mountains), on the west coast of India, is an important part of a world-wide program of monitoring biodiversity. To this end, a massive vegetation data set, consisting of 51,834 4-variate observations has been clustered into different landscapes by Nagendra and Gadgil [Current Sci. 75 (1998) 264--271]. But a study of such importance may be affected by nonuniqueness of cluster analysis and the lack of methods for quantifying uncertainty of the clusterings obtained. Motivated by this applied problem of much scientific importance, we propose a new methodology for obtaining the global, as well as the local modes of the posterior distribution of clustering, along with the desired credible and "highest posterior density" regions in a nonparametric Bayesian framework. To meet the need of an appropriate metric for computing the distance between any two clusterings, we adopt and provide a much simpler, but accurate modification of the metric proposed in [In Felicitation Volume in Honour of Prof. B. K. Kale (2009) MacMillan]. A very fast and efficient Bayesian methodology, based on [Sankhy\={a} Ser. B 70 (2008) 133--155], has been utilized to solve the computational problems associated with the massive data and to obtain samples from the posterior distribution of clustering on which our proposed methods of summarization are illustrated.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS454 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A potential cyanobacterial ancestor of Viridiplantae chloroplasts

The theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the evolutionary complicated Chromalveolates [chromista (cryptophytes, haptophytes, and stramenopiles) and alveolata (dinoflagellates, apicomplexans, and ciliates)] are inexplicable in the light of a single endosymbiosis event, thereby necessitating the postulation of the secondary^4,5^ and tertiary^6^ endosymbiosis theories where a nonphotosynthetic protist supposedly engulfed a red or a green alga^7^ and an alga containing a secondary plastid itself was engulfed^8^ respectively. In the current state of understanding, however, there is no clue about the taxonomic identity of the cyanobacterial ancestor of chloroplasts, even though there is a wide consensus on a single primordial endosymbiosis event. During our metagenomic investigation of a photosynthetic geothermal microbial mat community we discovered a novel order-level lineage of Cyanobacteria that - in 16S rRNA gene sequence-based phylogeny - forms a robust monophyletic clade with chloroplast-derived sequences from diverse divisions of Viridiplantae. This cluster diverged deeply from the other major clade encompassing all hitherto known groups of Cyanobacteria plus the chloroplasts of Rhodophyta, Glaucocystophyceae and Chromalveolates. Since this fundamental dichotomy preceded the origin of all chloroplasts, it appears that two early-diverging cyanobacterial lineages had possibly given rise to two discrete chloroplast descents via two separate engulfment events

Molecular markers assisted DNA polymorphism: Implications in mangrove research

Mangroves are defined as woody, evergreen group of plant community; grow on the swampy substrate at tropical and sub-tropical habitatsadjusted to high salinity, periodical tidal influence, strong winds, high temperatures, high precipitation and anaerobic soils. They possessunique morphological and physiological adaptive features to cope with these extreme conditions. Mangrove vegetation is the cradle of several marine fauna and provides first line of defense against devastating sea surges, typhoon, tsunami, etc. However, since industrial era, many of the mangrove members were affected by several environmental constrains and anthropogenic activities that raised the sea level, lowered sweet water influx from the adjacent rivers and encroachment for the new settlement formation, increasing salinity. Hence, mangrove restoration program is the front line topic of interest to the plant biologists across the tropical and subtropical world since it has a productive and protective role for the inhabitants. Sound knowledge of molecular characteristic of the individual taxa will be provide an advantage for this initiative.Recent advancement in molecular markers based on the PCR technique techniqueswill enhance the knowledge about genetic background of each individual taxon, ultimately leading to valid guided references towards the understanding the inherent nature of the plant itself and beneficial to proper restoration program

Environmental toxicity influences disease spread in consumer population

The study of infectious disease has been of interest to ecologists since long. The initiation of epidemic and the long term disease dynamics are largely influenced by the nature of the underlying consumer (host)-resource dynamics. Ecological traits of such systems may be often modulated by toxins released in the environment due to ongoing anthropogenic activities. This, in addition to toxin-mediated alteration of epidemiological traits, has a significant impact on disease progression in ecosystems which is quite less studied. In order to address this, we consider a mathematical model of disease transmission in consumer population where multiple traits are affected by environmental toxins. Long term dynamics show that the level of environmental toxin determines disease persistence, and increasing toxin may even eradicate the disease in certain circumstances. Furthermore, our results demonstrate bistability between different ecosystem states and the possibility of an abrupt transition from disease-free coexistence to disease-induced extinction of consumers. Overall the results from this study will help us gain fundamental insights into disease propagation in natural ecosystems in the face of present anthropogenic changes